Do you know if you were performing layouts on precisely the same diagrams on both servers, with IIS sometimes hanging?
If so, and maybe even if you don’t know for sure, I’m guessing that this is a .NET CLR/JIT bug.
I believe we have a special DLL for version 2.6 that attempts to avoids this problem. Version 3.0 includes such changes in the distributed kit. I don’t know if a modified DLL exists for version 2.5, though.