I had the same problem. After considerable frustration (from reverting to front-input), I discovered:
1) While Sound Max allows multiple mic-inputs, only one is permitted to be checked (active). How and why my choice of rear-input would revert to the front (mic) input during boot-up remains a mystery to me.
2) I could consistently keep the rear input active by un-checking the "microphone" (front-panel) option (i.e., allowing only the rear-input option.). I found this choice available in WinXP-Pro's ControlPanel/Sounds&Audio/AudioTab. Click SoundRecordingVolume. Choose/Options/Properties in the resulting window.. Unchecking "Microphone" and checking." Rear Input" forced my rear input to remain connected
3) Microphone Boost (Advanced) helped my mic's voice quality during Skype calls.