I'm not quite sure I fully understand, but when you are in Shutter Priority, it is its own mode (as is Aperture Priority and Manual Mode). What this means is when you switch from Shutter Priority to Manual Mode, your bodies will remember the last used shutter speed when in Manual Mode. The shutter speed from Shutter Priority won't carry over to Manual Mode (or to any other mode). In other words, each Mode will remember the last used settings when you were in that particular mode. Not sure if that addresses your issue, but that's the way I'm reading your issue.