ProjectX is a very useful tool. I scanned or demuxed the mpeg-File (don't remember), in the log of the process you get some information of the file!
You can also try pvastrumento to check the file!
At the moment i tried a trial-version of TMPEGEnc MPEG Editor to scan my files!
You can see a Graph of the file, faulty GOP's where diplayed in red (must be reencoded)!
But it don't support AC3 5.1 (reencodes it to stereo or AC3 2.1) !
Why nero's smart encode doesn't work with same quality and speed?
In my experience nero smart encode doesn't really work, it reencodes the whole file if something is not in spec!
BTW: There is no analyse-graph and no informtions that shows what is not ok!