Early-2014 Intel HD Windows 8.1 drivers have some bugs that give problems with f.lux, and you may not have the latest one (Surface Pro 3 does not as of September 2014). To make sure you have the latest:

The Catalyst Control Center is an optional component that can be uninstalled, and you might consider doing this if you're not frequently adjusting your settings for gaming or other reasons. Use Add/Remove Programs, and choose "AMD Catalyst Install Manager" to proceed. Do not uninstall the Install Manager , but instead use it to uninstall Catalyst Control Center. In our test, this didn't even require a reboot. Also, leave a note on this page (with the driver version) so we can report it to AMD.

Several people have reported that QuickGamma works well and produces good profiles that f.lux can read.

If you use a Spyder, the software profile loader may cause f.lux to flash periodically. You can disable the Spyder software on startup, and use f.lux instead to load the profile. Also, when you're calibrating a display, you'll want to do the opposite and quit f.lux before you do.