Hey Dan! For best results set ur RMX input/output to 12:30 so it's just lightly above the 12 mark- I've used it with the DJM600/700/750/800/850/900 & 2000 mixers with that setting and never had a drop in master output if i engage and disengage the send/return from the FX processor. I think you might have a problem with the cable- cause Pioneer mixers by default if there is no signal coming from the right it'll make the Left channel mono (it's kinda a fail safe system). Not sure if that applies to your setup- I use everything with 1/4" Jack to 1/4" Jack to connect the audio- others use the RCA-Jack connectors with no issues either. Ohhh have u checked the signal level switch on the back of the RMX?
Otherwise make sure you update to the latest firmware for the RMX1000 as initially there was an audio level issue with the BPF Echo (about a year & 1/2 ago got fixed). Try that out let us know- we'll try and figure it out for ya