There is a seal around the analyzer door and another o ring around the diff pump. Did you change diff fluid or something recently? If it hasn't been messed with in awhile I would doubt that it would spontaneously start having trouble.
What maintenance have you done recently?
You can try getting a can of compressed duster, check the CAS number on the back to find out whats in it (usually a halogenated ethane) and then go in manual tune and monitor that ion in profile mode. Spray the compressed gas around the seals of the vent valve, analyzer door, MSD interface and see if you get a big spike.
Another option is to stick a chunk of dry ice in a plastic solvent bottle and spray CO2 around those same trouble spots while monitoring ion 44.
Its interesting that you're not getting a constant leak, does it happen only when things are heated? Maybe your interface ferrule is cracked and you only get a leak when the oven heats up.
You may want to block the interface with a new nut and ferrule, vent the system and just stick the column in like normal and trim it a few inches from the interface and block it with a septa (or if you have a no-hole ferrule use that.) The system will pump down much faster than with an actual column installed and it will allow you to 'half split.'
Don't forget you could have a crack somewhere around the inlet, blocking off the MSD and leak goes away = problem is in the GC side.
I had a leak once that only presented itself with hydrogen carrier but if I switched to nitrogen it was fine, and only for low split ratios. Once I monkeyed around with the inlet enough trying to figure it out the leak got bigger and was happened regardless of what gas I used, but small cracks can be particularly hard to pinpoint when they only occur under certain conditions like high T.