All MP3's I have played so far have worked fine. Most are from eMusic. I have seen other reports regarding sound quality issues with sound quality with streaming internet radio.
Droid Bionic while trying to unbrick Droid Razr MAXX, Fascinate, original Droid
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I am on BB 0.4 with several 100 mp3 files obtained from a variety of sources (ripped from CD's, downloaded from web, etc) and have had no problems playing any of them (I use Meridian and 3 as my players).
Could it be an issue with your player and Froyo?
there's an app called "sdrescan" that does just that, rescans your sdcard so android media players and the gallery don't miss anything - maybe give that a shot?
This can't be only a Froyo issue because the rest of the rooted world would have gone nuts about this already. It only seems to be some of us. It would be nice if someone that isn't having this problem could address it and help us resolve it, or a ROM developer could tell us what might be wrong.
basically, if the gallery or music player sees .nomedia, it ignores anything in that directory (not sure about subdirectories - i think the file has to be in each specific directory and does NOT apply to subs, but not 100% for sure)
My issue was caused be a single MP4 video file. Phone would freeze up randomly and none of my music would appear. I discovered it by formatting my phone and adding stuff back to the memory card incrementally.