There are a number of configuration options you must make sure remain identical if you want binary compatibility to work. You have to watch out for a number of things, including, but not limited to:

• usethreads or useithreads (I forget which one is preferred).
• use64bitint
• use64bitall
• uselongdouble
• usemymalloc
• useperlio
• the option for adding malloc overwrite checks

If you don't use the same set of options as the previous installation, various C structures no longer line up correctly and you'll get strange and entertaining segfaults (update: in XS modules). Have a close look at Config.pm for each version and check for differences.