4.6.1 Beta exhibits exactly the same symptoms.
Well, more than likely your preferences were re-saved when you used PM 4.6 and you'll need to remove them and then they'll get imported when you startup PM 4.6.1.
You can find the PM 4.6 preferences file here:
C:\Documents and Settings\<your login name>\Application Data\Camera Bits, Inc\Photo Mechanic\com.camerabits.PhotoMechanic.prefs
Make sure you've quit PM first. Delete the prefs file. Then start PM 4.6.1 up again. It should import all of your PM 4.5.x preferences with the exception of FTP As snapshots.
-Kirk