After checking my computer over thoughly for the last 9 hours I belive I have stumbled on to the cause and solution to the problem... I thought I'd share it here as you guys tried to help me.
The issue is the fact that the game won't load except autosaves and...if you play the game for while it is...glitchy to say the least.
I will warn you now I am in the process of reinstalling my mods so I know this works for the unedited game...though if there are problems with tslrcm I will let you know....
The Solution: Turning off real time file scanning for those ever annoying guys mcafee... it will not allow the game to load all its files causing glitches and seems to have a peticular hatred for your savegame edited ones... you can also add the inividual save files to the exempted list but that does not help with the game glitches...(adding the swtor2.exe does not help). Given that there seems not other way to fix this problem (unless you come up with one) perhaps you guys could warn people about mcafee in the readme or something?