I think I had the same problem with my nitdroid neotalk. I installed nitdroid on the emmc so nitdroid considers /home/user/MyDocs/ as my SD card, but the standard media player also does not recognize files that are in there, it looks almost as if it just skips the .sound folder (which is where my music albums are). For me the solution was to simply search for another music player. I tried a few, and finally I ran into an app called Meridian which allowed me to select which folders I want to use, so I use that for now.

By the way, you stated you also had a problem with multiboot sometimes not showing up when rebooting? I also had this issue, and noticed that if you slide your N900 open while rebooting, multiboot will always show up.

Hope that helps, cheers!