We've just updated the entire Map Suite product line to version 126.96.36.199, which addresses the issues that were raised recently with assembly versions and side-by-side installs. For full details, please take a look at the latest post in our developer blog.
If our new builds today don't offer a solution to your problem, please feel free to post your comments or questions either here in this forum or on the blog entry.
Thanks for using Map Suite,
The ThinkGeo Team