None of your music apps look directly at the music files on your SD card. Instead, they look at a tagged database generated by a system process called "media scanner service" (android.process.media). Thus, if this process hasn't run, you won't see your mp3s in any music app, nor in fact your videos or images in the gallery. The media scanner runs at startup (reboot) and should also run once the SD card is remounted. Depending on how much music you have on your SD card, this process can take 20 or more minutes to complete.
So, for whatever reason, this background process may not be running. Reboot your phone and go into settings->applications->running_services. You should see an entry called media scanning service (may look different from within a custom ROM... I use rooted FRG01B). If it's not listed, it's not running. You can also use the market app "autorun killer" to see if "media storage" is running after reboot.
I don't know a thing about Lithium mod, but this process should be there. One way to jump start it is to download the market app "rescan media root" and click "re-enable media scanner." That might fix your issue.
Also, as Pat Hoge pointed out above, if the media scanner is running, you may simply have an issue with your SD card. I will add one thing to his comment... you could also have a bad (ill-formatted) mp3 file. This could kill or hang the media scanner service. In this case it won't be enough to unload and reformat your SD card and restore your mp3s, as you will be restoring the mp3 that hangs the scanner. You may want to remove all of your mp3s and just try a few to see if they get recognized. The fact that NONE of your ROMs scan the SD card for mp3 media, may in fact point to an SD card issue or a bad mp3 file on that card. It has nothing to do with your being rooted. We are all rooted in this forum and we see our mp3s from within our audio apps (at least I do). Neall