A couple of ideas considering your recent edits, although I agree it is a bit shooting in the dark…
I would use a tool like “Beyond Compare” to compare the .Net Framework files and XML files on both machines (“folder compare” profile).
Favour the binary level comparison to be perfectly sure… if both of your machines are local, it should be very fast.
You can also try to run Mark Russinovich’s Process Monitor ( http://live.sysinternals.com/procmon.exe ) on both machines and run the documentation building process.
This way, you will see which files are being read from and involved in the help file building process, and where they are coming from…
You will get a lot of output as it will show everything that happens in your system; you may want to disable registry and network monitoring, to only leave file monitoring, and also exclude any process unrelated to the documentation building process.
I’m not an help generation expert, but I would think that the text comes from the XML files, so you may want to put a filter on only showing the xml files as well.
If you can identify the files involved, then you might just have to copy them from one machine over to the other.