If you use a load-balanced environment, make sure the files are identical. Also make sure that the temporary files for asp.net (in the microsoft.net folder in c:\windows) doesn't contain a different file.
it's still strange though. I found a couple of the same errors on google but with different dlls, and no answer.
Is there any pattern to recognize in the errors at all? I.e. does it occur after the session expires? On a page which contains an LLBLGenProDatasource(2) control?
Looking at the forums.asp.net thread, it looks like it happens when the appdomain is recycled. When you browse the site, and force a recycle in IIS admin, do you see the error happening? (e.g. when you browse a page with data bound through our datasourcecontrol, so entities are serialized into the viewstate/session etc. )