In the end, I just ended up converting using Riverpast cleaner; but what you said makes sense about Squeeze having a tough time with different keyframes; I was thinking initially that it looked like a 24fps vid trying to play at 29.97fps (repeating keyframes like you mentioned). The video also had some time remapping, well, more of a strobe effect actually, so squeeze could have been having issues with that.
Thanks for the response Aharon