I'm not sure if this will help or not, but here goes....
We are using a 3 head HDP filler/capper, I'm not familiar with Custom Brew, but maybe there are some similarities. I have found that the absolute most important thing for fast & consistent bottling is to make sure the pressure on the dispensing tank is 2 to 4 psi lower than the CO2 going to the bottle filler. I watch these settings throughout the bottling day and have to adjust them as they will change as the dispensing tank is dropping in volume.
Also....our machine has a pressure switch for each fill head. Every few months I disconnect the plastic tubes running to the fill heads and clean out a pasty build-up that could throw off the pressure switch settings (and has before).
AND I should say that we are bottling soda - not beer. However, all the equipment we use is brewery style stuff...and all the advice I'ver been given is from brewers! Also our soda is carbonated to 30 PSI (at around 32 degrees F).....so we're running our bottle filler with very high CO2 levels.
Hope this helps!!