I have had similar problems with needle valves in the past. What has worked for me was to close the needle valve then open it to full flow (if you are using a diffuser make sure to remove it before turning up the flow), then adjust it back down to whee you want it. In my experience, it seems that something causes a blockage in the needle valve and cranking the CO2 up for a second blows it out.

I have also had luck by increasing the pressure on my regulator when changing from a single needle valve setup to a multiple needle valve setup.