Hello. Do you mean methyl tert-butyl ether?
I would look into other sources of the problems you are coming across. I had to go through tons of methyl tert-butyl ether a few months ago, and I never had any problems with it reacting with polypropylene containers. The degredation you are seeing could be the result of exposure to light, but I would doubt it... there is a window right near my hood and when it's not raining plenty of sunlight comes in.
If you really think it is the cap, you could put a septum on the vial instead and parafilm it to make a seal...