Nik - one thing that might be causing the problem is the alcohol... how long have you used that with Vallejo? My experience with alcohol based thinners like Tamiya, and Vallejo paint is they tend to flocculate (thank you Ross for giving me that great sounding word haha) when thinned with it... They tend to clot a bit and look grainy while in the paint cup is what I mean. Maybe this is what is happening? The larger size of pigment particles coagulated together would make it easier to block the paint path...
Have you tried soaking the nozzle/head in lacquer thinner for a bit and try it? In my experience any problem with paint flows I have had, have "usually" been fixed with a good cleaning... Especially on something with a small nozzle like the CM-C.
I'd try soaking it in lacquer thinner (just the nozzle and head), then using Vallejo only thinned with their brand thinner or distilled water and see what happens.
Let us know how that works!