I remember running into the same/similar behavior while working on some version of ActiveSync. It's been a while, probably more than a year. If my memory serves me right, it's registry related. However, I can't remember what exactly were modified to resolve this.
I would suggest taking the following steps,
- prepare a clean machine
- run the original ActiveSync installation
- run snapshot for the first time
- run the repackaged ActiveSync installation
- run snapshot for the second time to get the differences
- analyze the additional entries added by repackaged version