These notes look like they were part of an iffy MIDI file, when you get rests like that it will require some work to get the note lengths longer if you don't want them ending abruptly. Those r24r96's scattered throughout the first file is whats causing that. There is a way to fix it but it will require a bit of work. You can either fix this in a MIDI editor implying you used a MIDI. Give them their full length in an editor and run it through your mml converter, or you can replace the rests manually using the replace command in your txt editor. Your files here also loop bits the song multiple times. If you decide to manually change them, shrinking them down first can make it easier. As for channel 2, I assume you mean #1, I think it might be the random note ties that are tied to no other value.
There's a loose ^ in there and It looks like it needs to be tied to a ^96. Without that tie its throwing off the channel's tick values and causing it to desync over time.
Second file, same story, a loose ^ in your channel #2 as well as the stray r192, remove that and add another value and it should sound ok. The note lengths being too short can also be fixed the same way for the second file.
Edit: The second file might need to adjust certain rests as well. For #2 you can use...
this works just fine and is the proper tick length compared to the other channels.
I think a post layout goes here somewhere...