I found the exact problem now. Wow, I just spent 5 hours on this - though most of this updating my Windows XP 64 installation (last time I needed it was last June), then trying to install .NET 3.5 to test SharpDevelop 3.0, only to have the installation fail, so I removed .NET 2.0, which also failed, but googling for the error code I found a KB entry with a workaround that solved my problems: remove the drive letters from all CD-ROM drives (WTF???)
Back to your issue, the problem is that SharpDevelop.exe is a 32-bit process (Subversion AddIn and debugger are not yet 64-bit compatible) and uses 32-bit MSBuild; but booc.exe is marked as "AnyCPU" and runs as 64-bit process. 32-bit MSBuild tells booc to use the 32-bit versions of the .NET libraries, which of course fails in a 64-bit process.
You can solve the problem by marking booc.exe as 32-bit only. Open a command prompt, cd to the directory ...\SharpDevelop\2.2\AddIns\AddIns\BackendBindings\BooBinding, and run the command "corflags booc.exe /32BIT+". (corflags.exe is part of the .NET 2.0 SDK).
Alternatively you could also use corflags.exe to remove the 32-bit only flag from SharpDevelop.exe - the Subversion AddIn will be disabled automatically; the debugger will sort-of work but tends to crash and/or hang often after debugging (you could disable the debugger using the AddIn Manager).