No, the extensions are not relevant. Describe specifically what you mean by "go together?"
Moving the audio track so it lines up with video, as above, would normally be what's needed.
If moving the separate audio track is affecting the video (and likely its linked audio), lock the video. Right-click to the left of its track and LOCK TRACK.
Share your project and someone will take a look. It's not difficult, can be private, and is the best way to sleuth out issues.
Here's how... http://nch.invisionzone.com/topic/23659-tips-for-getting-help-on-this-forum/
If it contains sensitive material link it in a personal message (PM). Click the envelope above. It won't be passed on or retained.
Use FILE|SAVE PORTABLE PROJECT AS, not simply SAVE PROJECT, and don't forget to share it.