OK, that was a nasty one!
Indeed, like
@sneaker_ger noticed, mkvmerge searches for delays of up to 10sec. However, gMKVExtractGUI being more tenacious, fires up mkvinfo and tries to search the delay the hard way. Then 2 bugs emerged:
1. The mkvinfo output string was changed and I never noticed it till now!
2. That part of the code tried to find delays for all tracks, while some of them could already be found from mkvmerge (<10sec delays).
Those bugs were fixed and pushed in trunk, new version will follow sometime soon.
Thanks
@2-perf and
@sneaker_ger for your valuable feedback!