I already knew that splitting of MP3 files is broken. I wrote about it in the past, with version 1.0. A quick check in version 1.2 shows that it still doesn't work correctly.
Recently, I learned that FLAC splitting is also broken. The total number of samples in the output files is less than the number of samples in the input file. This means data was lost. There is also another minor bug which may actually be helpful: the MD5 value is not written to the file. This can be used to identify FLAC files may have been split using Medieval CUE Splitter, because "
flac -t" will complain about it.
So far, it seems that Monkey's Audio (APE) files split without any data loss. The number of samples is correct, and the concatenated audio data from the split files matches the audio data from the source file. This means that as a workaround, other lossless files can be converted to APE and split. However, this workaround certainly slows things down, and I can't really trust the program because of the other bugs.