Problem #2 with the Merge feature:
In testing other options to try and preserve all the chapter marks, I did a merge job using the MP4 profile. Both source files are MKV, but since the merge is done by the DVDFab converter, I expected it to simply convert them to a single MP4 output file. DVDFab SAID it was creating an MP4 output, but the resulting merged file is still MKV, no conversion was done, and no errors or warnings were shown!
(And the problem with no chapter marks preserved from the second file was not fixed either.)
Mauser
might try going into common settings - general settings - click the factory default settings button in
the lower left corner of the general settings area, restart dvdfab and retry the merge feature again and see if that helps.
also run your file through mediainfo and see if the chapters are in for the second file.