H264 2pass messed up private data for joining files

I've got several 2-part (two separate files) movies which I encoded as MP4, MPEG-4 AVC / H.264 using 2-Pass ABR (6.000 bitrate / 12.000 vbv max bitrate) from it's sources.

Now i wanted to join all 2-part movies into a single file using MKVToolNix - but unfortunately only about 20% could be processed, the rest resulted in a warning:

• The codec's private data does not match (lengths: 40 and 40).

These 80% play the first part correct and then show a blue/red/green screen where the the second part should be. The lengths are always the same - but it seems like the 2pass encoding messed up a tiny part, but which?

There's also a bug report on the x264-devel mailing list.

My question is now:

• Is 2pass encoding in general a really bad idea if you plan to join two files?
• What was going wrong while encoding? What messed up the encoder?
• What exactly does "length: 40" mean? Is there a free tool to inspect this parameter?
• Is there anything i could do with these already encoded files to get them together? Re-encode the second track one more time lossless? Which tool would you recommend here?