I've ran another backup and this time everything seemed to go well, according to the log, however two m2ts files apparently were a bad mux as they are 0bytes. When i try to resume the job, the same thing happens, two m2ts resulting in 0bytes (main movie being one of them). In the working dir all files (h264, audio, etc) seem to be ok with proper sizes.
Edit: Just ran another disc through bd-rb and right at the beginning, when it finished encoding a trailer, tsmuxer.exe suddenly crashed (encountered a problem and needs to close). The muxing seems to be buggy, if that helps in any way