Have you checked the "hide modes this monitor can't display" box in windows display properties? And stopped and disabled the AMD External Events Utility service (type "services" in the start menu)?
I'm unclear on the sequence of events here. As admin, you have a modelist showing only the modes you want. However, when you reboot, as admin, modes you do not want (31kHz) appear in the modelist. Some programs (retroarch) are capable of grabbing these resolutions even though you don't want them to. Which seems straightforward so far, and will hopefully be fixed by the above comment. But to fix this you're... what, logging out and logging in again as a different user? Also i'm confused as to how you mean the modelines go away, in order to reappear when you reboot? Or did you mean that you install only the modes you want, but then after a single reboot the ones you don't get added to the list and don't go away again before subsequent reboots?