The latest video driver version 3345 should keep mode persistence at all times. If you are saying the screen resets multi-monitor settings might be due to any power settings you have enabled through Power Options, Control Panel or your power options mode might be resetting multi monitor settings.
I've checked the power settings and all are configured to get max performance, my colleagues have
the same laptop and are also using Windows 8.1 and have no problems with the display resetting.
The only difference is that my system was upgraded from Win 8 pro to Windows 8.1 pro preview to
windows 8.1 pro (through store update).
Using the system with just a single display I don't experience the problem, only when using an extra monitor
it is like the monitor gets disconnected (cable removed from connector). Sometimes this happens several times in a row.
The latest version has been tested with multi-monitor options and no issues were encountered. I would recommend getting customized drivers from your computer manufacturer and check if your still have same problem: