Volume flux in my mix. Phase Issue? Comb filtering?

I have a large number of mixes that I did back when I was on Cubase 3.x that are stereo wav files. Recently, I decided to convert them to mp3 files (for the smaller file size). I imported the wav mixes into v. 8.5 and exported the mixes as a stereo mp3 with no effects or anything. Most of the resulting mp3 files turned out okay, but a couple of them have noticeable fluctuations in the overall volume of the mix, like the mix is going in and out, making the mp3 useless. I have no idea how to address this or fix it because I’m not even sure what causes it. It sounds like a phase cancellation problem, but I don’t know how phase would be introduced when I’m just converting a single wav file to an mp3. The wav files sound fine, BTW. Any ideas? Is this perhaps due to exporting the stereo mix versus going back to the original 3.x song folders and exporting each complete mix with all of the tracks? I’m not sure if that’s going to be practical. Thank you for any suggestions!