Lots of good suggestions so far -- diagnosing gremlins like this can be challenging. More info might help eliminate some variables.
When you are having the AF issue, what happens (or doesn't happen)? When you press the shutter button, does the camera try to focus, but then not release the shutter? Or does it release the shutter without trying to autofocus? Or does it literally do nothing (as if the battery were removed)?
When you say that you have another lens but that replicating the issue is a bit tough, do you mean that you are only having the AF issue with one lens, or do you mean that you have the AF issue intermittently with both lenses?
Do you always turn the camera off before changing lenses (or removing and reinstalling the same lens)?
Alternatively (or in addition), if you have a neighborhood (or neighbourhood, if you prefer) camera shop nearby, maybe they can take a quick look to see if there is anything obvious.