Keep in mind the 315mhz frequency that's used for fob communication to the car is used by practically every other RF remote around. It's possible for it to have interference, which is why the have the Electromagnetic (RFID) bypass feature.
You often see this on the labels of these systems (probably in the owner's manual): "This device complies with Part 15 of the FCC Rules. Operation is subject to the following two conditions: (1) this device may not cause harmful interference, and (2) this device must accept any interference received, including interference that may cause undesired operation."
In this case the "undesired operation" is it not working.
Also note that the MCU doesn't control the fob/security system, so rebooting it has no bearing on it. The fobs are managed by the body ECU located in the passenger footwell. If you don't believe me, pull the MCU fuse and you'll still be able to lock/unlock the car, handles present, etc.
If you ever can't get into the car, take the fob to the passenger side cowling and wave the fob around there. The pickup coil is in the passenger side fender. Once inside the car, the pickup is in the center console below the cupholders.
- - - Updated - - -
I usually put keys on right side of my pant pocket and car key fob on the left side to avoid confusion.
On a parallel note have you all noticed that the magnetized cards (key access to hotel rooms) does not work if you drive with card in MS?
If this was true, we'd likely all have non-working credit cards all the time as well. It's more likely that most of those crappy mag-stripe hotel locks are just problematic. The car would have to emit a massive magnetic field to erase a magstripe card, and we'd have other problems. There is very little stray magnetic energy running around the car. (This has been beaten to death over and over again starting with the first hybrids.)