Yes, I had it happen at times before.
I'm stock and use handcent sms and a few other apps that give you the choice of having that app have unique ringtones, while everything else uses what's in the system settings sounds.
I tried copying ringtones to the internal, but still persisted. For me there was a simple fix (I wanted the mp3 ringtones I had made myself ) to use my custom ringtones from the sound settings menu.
First, I setup my custom ringtones in the system sound menu settings.
Second, from the app (in my case one was handcent) I choose the option in there to select ringtones and I chose the system picker as the default "picker" instead of the app as default app. Then - when choosing which sound to play - rather than "default", I choose the same costum ringtone I setup previously in the system menus.
I noticed that initially if I had picked only "default" and had thay specific app as the default app to do the task, my ringtones would often reset to the true system default.
Anyhow, hope that makes sense. It works for me & I'm no longer scratching my head as to why in the heck my ringtones/notification sound reset all the time - they're fine now and remain how I selected them to work.
Sent from my primary sender for sending.