Not one for doubling up, wanted to point to an early thread that might offer solutions: http://discourse.techart.online/t/python-maya-startup-script/2145/21 via @bob.w:
My gut is that PYTHONPATH is being set on Maya start up, but some higher priority tool, plugin, is overriding it prior to calling the userSetup.py. Can you attach a debugger to Maya and see what its calling on startup?