I make songs by doing the drums, bass, and keys in FL Studio and then recording that in Audacity, while playing the guitar over that... so I have the FL Studio song and the guitar in 1 track (unless I record 2 guitar parts, but whatever). Does that make sense?

Anyway, Audacity is deciding to only record the guitar and nothing from other sources. Plus, I can't hear the other recorded tracks while recording a new one, so everythings out of time.

Anyone know why or how to fix this?

can you not set the one track to record from the midi and then the other (guitar) to record from the wave in?