I experienced (twice) a failure in my Windows 98 network stack after installing the Freedom client - it apparently replaced/modified/removed some DLL component which was important to 32-bit Winsock connections, which meant that Eudora and web browsers stopped working.
Freedom's trying to do some pretty ambitious things in interfacing with the windows stack from within the tcp stack and transparently re-writing and redirecting packets at that level. That area of windows isn't the best documented. If you were using an early version things may have improved a lot since then. Also I think win2000 stuff is more amenable to the things freedom is trying to do.
In the past year considerable resources were affected to increase the ease of use and to resolve compatibility issues with Freedom. Improvements in the interoperability area, improvements in the qa testing area, and alot of refactoring has greatly improved the overall quality. So yes, it has improved alot. Any 2.0 installation woes during Beta were far and few between. Mario Disclaimer: as always these are my personal comments.