Okay so I did some digging and basically I found out that none of the SPB programs are actually approved for WinMo 6.1. I suspected something was odd when I uninstalled everything and reinstalled PP and PS, both came up as registered, which has never happened, and there were several features not installed (Smart Scrolling, the ability to reject a call and reply with sms for example).

So I did a hard reset and all the issues I was having cleared:
-I can now recieve text messages when the device is asleep
-The status light always blinks
-The battery shows less than 100%

So, for what it's worth, if you're having any problems and have SPB programs installed, I suggest that's the first place you start looking. They are trying to fix PP to be fully functional with 6.1 (and my PP worked fine until I installed the rest of my SPB programs) so there's hope. I'm going to give it a good week without any 3rd party apps (except icontact and live search - both I know to work fine) and see what happens.