They had to redo the widescreen and higher resolution support, etc, for the 1.006A release. I haven't seen a list of changes or fixes, but believe they just focused on technical issues. It isn't a case of re-creating omissions, just lack of resources to do everything over again.
They didn't redo the changes to the weapon expertise skills, for example, made in the 1.004A release (all skills switched to percentage based damage bonuses) but which reverted to the earlier version with the 1.005A update (ie some percentage based and some fixed range damage).
EDIT: I can not seem to post a new reply, so...
From the corresponding topic in the Larian forum;
"I can understand your confusion - the version on GOG and the version on Steam are different ports due to an accident at Larian that caused us to lose the source code of the GOG version. It's a pretty stupid thing, but sometimes things go wrong. So to make the Steam version, the port to adapt for Windows 7, had to be redone. Therefore, there's no relation between the GOG version and the Steam version, other than they're based on the same original game.
We're going to look at what issues might appear if we release the Steam version on GOG, and if none show up, we'll make it available there too, just to make future updates easier.
Sorry about the confusion."
Post edited July 06, 2012 by Raze_Larian