The first thing you're describing is normal. If you leave the bloop on and turn any pedal(s) in the loop off, you're then getting a mix of your full-range signal (from the loop the disengaged MojoMojo is in) and the Bloop's low-passed clean signal. In other words, if you've got any pedals in the loop disengaged, it's the same as just running a patch cable from the send directly to the return on the bloop. I believe they've even got this in the manual as a way to use the Bloop.
Assuming everything is wired correctly on your board, the thing that doesn't make sense is "If I switch the Bloop off it acts as a mute. Mojomojo is going into the send/return here." Bypassing the Bloop should do just that - not mute. That sounds like either there's an issue with how you've got it wired/powered, or maybe an issue with the pedal in bypass mode, as it's not passing signal.
An easy way to isolate and test the bloop is to take it off your board and just run the bloop between bass and amp. Bass to Bloop "In" and Bloop "Out" to Amp input. Then run a single cable from the Bloop "Send" to Bloop "Return". With the Bloop turned off, you should be getting your raw, unaffected bass signal. If you turn the Bloop on, you should hear the low-passed blend come into play and turning the blend up should beef up the lows/low mids in your signal.