Here's the quickest way to get away from using the Wavetable synth; should deliver comparable (possibly better) sound quality:
- Open the MIDI File
- Insert > Soft Synth > Cakewalk TTS-1
- Ctrl+A to select all tracks.
- Hold Ctrl while re-assigning the Output of one MIDI track to TTS-1 (re-assigns the output of all selected tracks by Quick Grouping).
- Import the audio.
- Play
Assuming the tempo of the audio is perfectly matching the project (not usually a good bet), you should hear everything, and it should be in sync. But note that MP3 files always have a few milliseconds of 'dead air' at the front due to the encoding process that will cause the audio to be a little late relative to the MIDI-driven soft synth. This can be easily corrected in SONAR by zooming in, slip-editing the start of the clip, and dragging it back to 1:01:000 (or wherever the first note should hit in the timeline).