agree with trans, how are you going into the profiles to save? let us know the path you're using and we can try it and see what we get...
also, try using a different tone?
one other thing, when you saved the "media" onto your phone, did you let it scan the media and create a bbThumbs.dat file?
go to where the media is by following media>explore>memory card (or where ever you saved it).....blackberry>ringtones and bb button>show hidden and find the bbThumbs.dat file and delete it, then reboot, when it powers on it should re-scan and create a new one. if that file is not updated it could cause a lot of issues, like the profiles not contacting the proper media directory and when no sound is found it plays the default ringer.
do you have your phone plugged into the computer when it just beeps? If you have Mass Storage set to yes and its plugged in then the phone can't get to your card to play the custom ringtone, thus it will default to a beep.
When unhooked it will work perfectly again.