So in 10.10, there was no problem with the notification area. But after upgrading to 11.04, I got this weird system-colored background behind the Music Note banshee uses as the Notification Area Icon.
Is there anyway to get rid of it? Thanks :)
The non-transparent panel background bug was an unfortunate side effect of a workaround to fix a different bug that was causing Banshee to crash. Luckily, the workaround is no longer needed, so it was removed on May 7 (which should fix the icon issue). There hasn't been a stable release of Banshee since the 7th, but the problem will go away with the next release.
If you want, you can manually remove the workaround that caused this problem. To quote the bug report,
Note that this problem only happens with the standard Notification Area icon. If you don't want to manually edit any text files or wait for a new release, you can always use the Banshee Application Indicator or Sound Menu integration instead of a traditional notification area icon.