This is a web development forum, but to somewhat answer your question there is a scheduler in Windows that runs programs at specified intervals (not that I've ever used it). For one it can be used to run the program automatically (removing the need for the bubble), but if that's not desired you can just make a batch script (simple stuff, Google it) that runs on the schedule and basically just outputs a message (and pauses so the prompt doesn't close). It's not a bubble, but it's a window with a message and has the same effect.
There are probably some people who actually knows Windows programming here that can help you though (I'm a Linux geek), so if my ad hoc solution doesn't suit you wait for (and hope that) someone else pitches in.