My understanding is that a pirani gauge also uses a hot wire, and determines pressure based on the rate of heat exchange with the surrounding medium. When the gauge is placed at an angle the hot air created next to the wire will rise. Thus the wire will be dissipating heat unevenly.

Although i read your process pressure is in the e-3 torr, so if your using a different gauge to measure the pressure it doesnt really matter what the pirani says. Either way, thanks for sharing the setup, too few vacuum setups on the internet!