Okay, having looked via search an things on the forums I noticed people had similar problems with v1.x.x but that these problems were fixed in v2.x.x.
Yet for some reason I just installed a fresh install of v2.0 yesterday and uploaded the entire roster that was saved with a fresh scan/save of both Character & Guild Profilers. Confirmed they were all entirely uploaded and went to bed. I just logged in to see that the entire roster was wiped and was getting error messages about no guild found, etc.
Anyone else having this problem or is it just me?
Also, anyone have any ideas how to fix?