By defaulted back to unprotected do you mean you had to manually set them to protected again or just that their counter restarted? When the server is updated/restarted all passive timers are reset. The mod author stated a while back that he fixed that issue when in fact all he did was make it so passive protected tame timers can count while not being rendered.

If it wasn't the timer, but rather the protection toggle then no I haven't seen that problem reported before.