Thread Subject: Local pause alternative?

For various reasons, I've written a GUI front-end for communicating with multiple and different serial devices. The low-level communications protocols for each of the devices means that you have to use pause(x) to make sure e.g. data has arrived when it should do, and that commands are not sent too quickly. The problem is, pause(x) interrupts everything in MATLAB, which is fantastically annoying.

I'd like to know if anybody has managed to come up with a local pause function, a "rest" if you like.

The only other way that I can think of doing it is by breaking up the function into pieces at the places where I'd like a pause, then use a complicated set of timer objects and pass the data through to them all, which is obviously more awkward.

Any other suggestions?