that was my biggest problem with the smaller prizm, and the reason i returned it - like you are experiencing - I had to turn it up higher to collect anything and thus produced so many micro bubbles. the larger prizm pro has more turns and a longer distance for bubbles to travel, thus preventing most bubbles from leaving the skimmer. People place "bubble filters" on skimmer returns a lot, preventing bubbles from going back into the tank. You may be able to do the same on the prizm, I don't know. Maybe you could try putting a pad/sponge or something the the output side of the discharge - might catch the bubbles, but might make it overflow over the sides too.
And to clarify - you don't want "clean" water collecting in the cup, just skimmate junk - brown crud. if you are getting clear water, you have it flowing too much anyway and need to turn it back. If you aren't getting any crud at all, most likely not enough flow, but maybe your tank is super clean too.
Well, let me know how it goes...