Apparently SRX creates a display override that applies your setting. This override must be loaded every time the display is used and monitor's device ID is detected.
Pasted from their FAQ:
"If you can't see the Finder or can't start SwitchResX Preferences itself, you'll have to delete the monitor profile file.
This file is located in /System/Library/Displays/Overrides/ and is the last modified file, that you can find if you sort by date. You should remove this file, if you can access the file system, either by
1) accessing the file system from an other Mac on the network, via Remote Desktop, from ssh or by mounting a shared folder.
2) OR starting up in single user mode
3) OR via Target Disk mode if you have an other Mac
4) OR at last resort: reinstalling the OS above the existing install, which will keep your existing settings, but remove the system modified files."
Pasted from their FAQ:
"If you can't see the Finder or can't start SwitchResX Preferences itself, you'll have to delete the monitor profile file.
This file is located in /System/Library/Displays/Overrides/ and is the last modified file, that you can find if you sort by date. You should remove this file, if you can access the file system, either by
1) accessing the file system from an other Mac on the network, via Remote Desktop, from ssh or by mounting a shared folder.
2) OR starting up in single user mode
3) OR via Target Disk mode if you have an other Mac
4) OR at last resort: reinstalling the OS above the existing install, which will keep your existing settings, but remove the system modified files."