Thanks to Rootzwiki developer erishasnobattery (again) who confirmed the bug, we now know that the reason why some of you may be missing your ringtones, pictures, videos, and audio files. ROM Manager, in its 126.96.36.199 update, placed a file called .nomedia on the root of your SD card, which causes the media scanner to skip the entire SD card when it scans your phone for media at startup. This will not only hide your ringtones, but also all of your other media files (don't worry, they're still there on your SD card, only your phone doesn't know it). ClockworkMod, the developers of ROM Manager, are aware of the issue and tweeted that the issue has been fixed in the 188.8.131.52 update now available in the Play Store.
Erishasnobattery also provided this workaround in case you still don't see your media files: delete the .nomedia file on /mnt/sdcard/, clear media storage data, remove ROM manager, reboot.
How to clear media storage data for those of you who don't know:
(1) Find Media Storage in settings/apps/all apps, (2) open app info by tapping on the Media Storage icon, clear data