Do they just disappear all of a sudden? Are you sure you didn't just hide them in the phone application? Try swiping from the left side of the screen towards the middle while in the phone application.
Interesting. I hadn't even thought to do that. I've rebooted my phone already but the next time it does that I'll have to try that.
You should be able to swipe the speed dials to the left to make them disappear. Try that and see if that's what you were seeing before.