mkvtoolnix gui split files keeps adding extra few seconds

I am getting the above three errors/warnings with almost every file mkvmerge is creating for me. This usually indicates a damaged file structure.

'Warning: kax_reader_c::read(): an unknown exception occurred. 'Warning: The first cluster timestamp after the resync is. 'Warning: The last timestamp processed before the error was encountered was 'Error in the Matroska file structure at position. Just for kicks, if I try to append the segmented files back together, then mkvmerge will produce the error when it gets to those spots reading the file: Sometimes audio continues without video, sometimes it is just completely frozen. If I play the newly created file back, it will hit one of these corrupt locations and stall for several seconds before catching up. But what I'm finding is these segments frequently have corrupt sections (not at all related to the split points). mkvmerge produces no warnings or error messages and appears to create the segments perfectly. I am not making any other changes to the file (e.g., same codec, all streams, no manipulation whatsoever). I am using mkvmerge to split the file into smaller chunks. I know the source files are sound because they play fine. I have been using mkvmerge recently to split up segments in my movie files.

Mkvtoolnix gui split files keeps adding extra few seconds