At early 2013 I've discovered problem in Just Cause 2 and other games, that stopped my game progress.
The problem was so unusual, that I belived at first, main reason is the hardware.

With some digging in pain, many hours later, I've got answers for my problems and I would like to share them.

First symptom was Just Cause 2 starting, but not fully loading, not even going to menu.
Just small logo rolling forever in the right bottom corner..

During investigation with Square Enix support I've discovered, that this problem is outside game,
lies on operating system level, at filesystem, between Steam and NTFS.
For more information go to the original thread.

Let's see.

First of all, only Windows users are affected. I don't know about Linux or SteamOS issues here.
Let's say You have installed Steam in following folder:
D:\Games\Steam
and files of Just Cause 2 resides in
D:\Games\Steam\steamapps\common\Just Cause 2.

If this is unusual volume, NAS/DAS/SAN or RAID, or anything with large capacity, then check if it has correct NTFS properties.
Open elevated command prompt typing by cmd in Start menu, then right click on it "Run as Administrator".

Next type following command:
fsutil fsinfo ntfsinfo d:
Correct output is similar to this:
NTFS Volume Serial Number : 0xsomerandomnumbers
NTFS Version : 3.1
LFS Version : 2.0
Number Sectors : 0x00000000e8e077ff
Total Clusters : 0x000000001d1c0eff
Free Clusters : 0x00000000004b6091
Total Reserved : 0x0000000000000060
Bytes Per Sector : 512
Bytes Per Physical Sector : 4096
Bytes Per Cluster : 4096
Bytes Per FileRecord Segment : 1024
Clusters Per FileRecord Segment : 0
Mft Valid Data Length : 0x000000002d200000
Mft Start Lcn : 0x00000000000c0000
Mft2 Start Lcn : 0x0000000000000002
Mft Zone Start : 0x000000001795a120
Mft Zone End : 0x0000000017965a60
Resource Manager Identifier : SOME-RANDOM-LETTERS

If returend value for Bytes Per Sector is larger than 512 bytes, then You're affected and Your game will not work.

UPDATE:
You can also extract only valuable information using command:
fsutil fsinfo ntfsinfo e: | find "Bytes Per Sector"
not-affected volume just returns:
Bytes Per Sector : 512

So far, since time of discovery around April 2013, there is no workaround.
You must move Steam folder to different volume with different NTFS properties.
I've opened two Support Tickeds, both were closed without solution.

Sector sizes like 4kB, 8kB, 16kB which can be set at storage system level will block game from loading.
Advanced format disks with 4kB remains unaffected, because they mostly return compatibility mode cluster size: Bytes Per Sector: 512

If You want to test if issue is really existing, the easiest way is to install Oracle VirtualBox
WARNING: You'll need to re-enter Your password in Steam account, as metadata is refreshed.
DO NOT PROCEED IF YOU DON'T REMEMBER CURRENT PASSWORD.
1. download Oracle VirtualBox[www.virtualbox.org]
2. download FreeNAS[www.virtuhttp]
(at bottom of the page click on "No thank you, send me to the Download page please."
3. deploy FreeNAS with following parameters:
General tab
name: FreeNAS
type: BSD
version: FreeBSD (64-bit)
System tab
Base memory: 8192 MB
Boot order: marked only: Hard disk, Optical - within this order, no other selected
Processor: at least 2
Acceleration: Enable Vt-x/AMD-V should be marked and feature enabled in BIOS
Audio tab
disable all audio devices
Storage tab
Controller: IDE
Create hard disk FreeNAS_OS.vdi with at least 8GB capacity.
Controller: SATA
Create hard disk FreeNAS_data.vdi with capacity of all game and Steam files (Just Cause 2 takes around 5GB so 6GB at least)
Network tab
Adapter 1 - NAT
Adapter 2 - Host-only adapter
4. Install FreeNAS in VM
in VMsettings, at Storage tab, select controller IDE with CD Empty icon, then select downloaded .ISO of FreeNAS
Right control in VM window frees cursor back to OS
Choose 1 - Install/Upgrade
choose first disk - 8GB with Space key
set some easy to remember password, wait until install is finished
select 3 and reboot VM
First boot will take couple minutes because SSL certificates are generated.
5. share iSCSI disk
After reboot, set networking for FreeNAS:
DHCP for first network card (NAT)
static IP 192.168.56.101 for second network card (Host-only) with netmask 255.255.255.0 and no gateway or DNS (if DHCP doesn't work)
Go to web browser and type internal IP address:
http://192.168.56.101
login with username root and password set at step 4
Go through initial wizard.
skip with Exit button at Active Directory step
Now goto Sharing -> Block (iSCSI)
Add portal on internal interface
Add Initiator for ALL
Add target with name like "disk1", selecting previously created group and initiator, no auth method
5a. Now, most important step, add Extent with name like "ext0" type: device, selecting ada1, with Logical Block Size different than default 512 bytes, ex. 4096 bytes
5b. Finally, assign Target to Extent
Goto Services and switch iSCSI to ON
6. Now connect to iSCSI target. You'll need iSCSI Initiator installed.
Goto Windows "Control Panel", search for iSCSI
You'll be asked for enabling service, select Yes, then click icon again.
Now, on the second tab - Finding (or similar) click on "Find portal"
type IP of FreeNAS internal interface, 192.168.56.101
if You have multiple network interfaces installed it's better to manually select correct outgoing interface via Advanced
Now on the first tab "Target elements" or similar click on target and Connect
Unmark "Add to favourites" as this can generate large number of error log entries if target is unreachable.
Now, if the status is Connected You're ready to format new virtual drive and copy Steam files on it.
7. Format drive via Computer Management -> Disks (with completly default settings)
8. copy Steam folder to new place (or install completly fresh, then restore game from backup)
In case of Just Cause 2 following files and folders are important:
D:\Games\Steam\steamapps\appmanifest_8190.acf
d:\Games\Steam\steamapps\common\Just Cause 2\*.*
d:\Games\Steam\*.* except folders steamapps, userdata
d:\Games\Steam\steamapps\*.* except common, appmanifest_*.*
Saves will be provisioned from the Cloud or just copy userdata\8190 to the second location.
9. Close Steam from primary location. Start Steam.exe from virtual volume. Start the game.

Affected volume returns:
fsutil fsinfo ntfsinfo s:
NTFS Volume Serial Number : 0xsomerandomchars
NTFS Version : 3.1
LFS Version : 2.0
Number Sectors : 0x000000000027ddff
Total Clusters : 0x000000000027ddff
Free Clusters : 0x0000000000278ddd
Total Reserved : 0x0000000000000040
Bytes Per Sector : 4096
Bytes Per Physical Sector : 4096
Bytes Per Cluster : 4096
Bytes Per FileRecord Segment : 4096
Clusters Per FileRecord Segment : 1
Mft Valid Data Length : 0x0000000001b00000
Mft Start Lcn : 0x00000000000c0000
Mft2 Start Lcn : 0x0000000000000002
Mft Zone Start : 0x00000000000c0000
Mft Zone End : 0x00000000000cc820
Resource Manager Identifier : SOME-LONG-ID
.. and game no longer loads.

Integrity check in Steam Library will return status 100% ok, but the game will no longer work.

All Steam versions from:
Steam client Oct 9 2014
API: v017
package version: 1412887979
to:
Steam client Dec 19 2016 (18:21:07)
API: v017
package version: 1482202200
seems to be affected.

All versions from
Windows Vista
to Windows 8.1
seems to be affected.
Windows 10 was not tested so far.

All Steam versions of these games seems to be affected:
Just Cause 2
Saints Row 2
Saints Row: The Third
Carrier Command: Gaea Mission