I don't think that the PC is the problem ... it's a Lenovo ThinkPad T520 with an Intel Core i7, 16 GB memory and is running on Windows 7.

As far as I remember you once mentioned that in debug mode internal xml data is built up ... can it be that there's a problem?

Is there a way to check for broken files by tool? Our project consists of such a high number of files that it might get hard to find a broken one.
Is it for example possible to write some more information into the logfile while SED (or the engine when started with -debug) is compiling data / loading files? So that would be an indicator to the broken file.