Sorry to dig up a slightly old topic, but I have this EXACT same problem in my '97 Boxster. Mine rarely works 100% though.
If you have solved it, please let me know as it really sucks
This is what my car does.... if the car is locked, I put the key in the drivers side door, and when I turn it, it will only unlock that door, but not the passenger or fuel door. In order to unlock the rest of the car, I have to either open the passenger side door from the inside (which will make the car beep twice and turn on the interior lights, while you hear the locking mechanism working), or push the unlock button on the dash, which will just unlock the pass/fuel doors but not make the car beep.
This has been going on for a few years, I've just learned to deal with it since I definitely don't have money to spend on a shop to try and find the problem. The week after I got the car I had an aftermarket radio installed, so maybe that has something to do with it.
I honestly forgot about it until I got back on this forum, and was going to post a thread until I found this one.
If anyone has any suggestions or needs more info, please let me know.