I have Retry System (+ multiple checkpoints) v2.06a installed and believe this is whats causing the conflict.
My quick retry is working properly, but im running into issues with my midways.
I have a level with a pipe that brings you to another level. At the start of the 2nd level i put a midway point and a midway entrance. instead of starting at the midway entrance it takes you to the pipe at the end of the first level.