You ever go to make a CDLC and in the guitar pro file you are trying to import there is unnecessary sections added to the song? Wondering if there is a way to delete individual sections because it throws the whole rest of the beat timing off for every section after. 

Are you sure it's sections that are causing your issue? Cause sections shouldn't alter timing in any way.

If I understand it correctly, section placement matters for DDC. I don't expect it would affect note/chord timings.