I think there may be a bug that occurs when pausing renders, which allows it start caching GI based on what's in the preview, not the full render. So when you unpause it continues with modified GI. Obviously this is bad, and I need to fix this. However, I believe it only occurs if your preview is in non-RTP mode, because non-RTP mode can resume rendering while the main rendering is paused, whereas RTP mode doesn't do this yet.
Matt