Raze there may be something to this idea of old bugs returning. I've been looking at the forums on Good Old Games and there are some unusual complaints about bugs that were fixed by patch 1.0033:
http://www.gog.com/en/forum/divine_divinity_series/having_issues_with_main_questMainly problems with NPC's becoming hostile, but causing problems with giving Slasher back, and with Zaknadrix the imp's dialogue.
I have the download version but haven't given it much time because of a relatively minor bug (music transitions are missing). But seeing as how I have all versions of DD installed I wouldn't mind taking the time to check up on this, if I knew how.
Tarnum can you clarify how you're comparing files between the versions and how you're verifying that older/outdated files are being used?