You mention switching from the .35 to the .50
needle, but are you also swapping out the paint tip (aka "fluid nozzle") and regulator (aka "nozzle cap") with the corresponding ones? Perhaps that is implied but I have to ask as if one were to use a .5 needle with .35 head parts, well, that would explain a lot.
Anyway...
To try to be a little more analytical here...bubbles in the paint cup means that, at least in part, air is finding it easier to work its way backwards from its outlets on the front of the AB body into the paint chamber/cup. It really has only one way of getting there: either through or around the paint tip .
IIRC the HPBCS uses a tapered seat paint tip like most Badgers. That means that the only way for air to get past it is if its not seated firmly and correctly. A
badly bent needle might force it out of alignment but I'm more inclined check the orifice it sits in on the airbrush body. Even the slightest contaminant there will cause the tip to not seat properly and provide a short-cut for air to get back to the paint cup. Dig, and I mean DIG at the seat with a qtip soaked in pure booze or Vallejo's Airbrush Cleaner.
As a side note, I find Windex to be much too weak for AB cleaning of acrylics. I use alcohol for the flushing and Vallejo Airbrush Cleaner for the finishing.