I found this one tonight by coincidence and it is the same in both 1.17.7 and 1.17.8. This is on the bluray disk for Supernatural S2D2. This disk is weird in that it has one title with episodes and the like broken down by chapters. MakeMKV shows this is 8 different titles, with some being 00100.mpls(n) where n is 1-4.
When I process the disk with the GUI, the output file *_t03.mkv shows up as "00100.mpls(3)". When I run a makemkvcon64 with it, it shows that it is instead "00100.mpls(4)". I noticed because it's messing up my autorip code since the mpls filename doesn't match up with what I put in. I'm working around it manually for now, but if there's any info I can provide to help, please let me know.
Data mismatch between makemkvcon64 and gui for 1.17.8
Re: Data mismatch between makemkvcon64 and gui for 1.17.8
Update: There is something weird going on depending on how it's called. I'm digging for more info now, but it seems that looking at the output of makemkvcon64 with "makemkvcon64 | more" gets a different response than redirecting output to a file. No clue how this could happen though. Will update if I find out more.
Re: Data mismatch between makemkvcon64 and gui for 1.17.8
Update 2: It seems it might be a random error from the drive as it works on another drive. If you would, please close/delete this one as it was a hardware issue.