Actually, the inability to play gapless is THE biggest issue I have with the MP3 format. MPC and OGG play perfectly gapless, and all lossless formats (obviously) too. As other people have mentioned, it's not a MJ issue, it's a fundamental shortcoming of the MP3 format itself.
I have tried several things, but I never got a solution that I was 100% satisfied with. Crossfading with 0.1 seconds, as ZRocker mentioned, is the best workaround I found, but the result is not 100% satisfactory in all cases. The timing (rhythm) can be slightly wrong with some tracks.
I am forced to use MP3s for my portable player, but I'm eagerly awaiting a player that supports OGGs. Then I can finally drop MP3 as a format for my music altogether.
I don't know if there's anything MJ could do to solve it. Maybe adding 0.01s crossfading could help. Maybe an "experimental" gapless plugin, where the plugin detects and removes silence could help. I don't know, but I would guess that, if there is a good solution for it, it would have been found by now.
Edit: I didn't read you original post thoroughly enough, and snipped some useless explanations.