RX2 playback issues

I have read a few threads about this issue, but so far haven't come across a concrete answer. Last night, I wanted to record a mix, I practiced the mix which took an hour, I then recorded the same tracks using usb port 2 to read and write from. About 4 instances throughout the set, I would try to load a new track and the screen would just say "wait..." with a spinning circle for approx 2 mins. Upon replaying the recording, in the moments this "wait..." was displayed on the screen, the playback of the current track playing went very choppy and was jumping around to different parts of the track, totally ruining the mix. I would like to know if this is likely an issue with the USB stick I used, whether its better to use one port to read from and one to write to, or if it is likely to be a deck firmware issue or even something else? Any suggestions would be very welcome. Cheers.