I only want it to revert to "frequency use" rules
Using the "Remove from this list" menu item does not change the rules used. All you did is zero the usage counters of your application; it should re-appear in a couple of launches.
If it doesn't, try:
reg delete HKCU\Software\Classes\Applications\cmd.exe /f
reg delete HKLM\Software\Classes\Applications\cmd.exe /f
reg delete HKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\UserAssist\{75048700-EF1F-11D0-9888-006097DEACF9}\Count /f /v "HRZR_EHACVQY:%pfvqy2%\Npprffbevrf\Pbzznaq Cebzcg.yax"
reg delete HKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\UserAssist\{75048700-EF1F-11D0-9888-006097DEACF9}\Count /f /v "HRZR_EHACNGU:P:\JVAQBJF\flfgrz32\pzq.rkr"
taskkill /im explorer.exe /f && explorer.exe
...or clear the program list and re-fill it with the most used programs.
...or simply pin it there.
If you do want to forbid a Start Menu item from appearing on the Frequently Used Programs list, use TweakUI → Taskbar and Start Menu → Start Menu and (un)mark the program.