This is a known bug with Womble. You have to overlap the two audio tracks that you are crossfading and apply at least a three-frame fade out to the first audio track and a three-frame fade in to the second.

If you do not do this, the pop might not be in the preview, but it will be in the exported file. Womble is a pain sometimes.

When you say you have two video tracks on the timeline, I take it you mean one next to the other on the same track, but they are from different sources rather than the same source. Are you working with muxed audio?

Another thing that helps is making sure these options in Womble's options are checked:

Gop size compliance for DVD recording;
Use CRC protection;
Re-encode the whole audio if any part needs fixing.