I'm not certain I can help, other than confirming that yes, the E-Mu Proteus modules definitely respond to expression via MIDI. And the response is global, not just per patch (so I don't think your answer is in the PatchCord parameters) I have an E-Mu B-3 module which I used to use for that all the time. (I slaved it through a DX21). I have since gotten a Proteus V6 keyboard and moved the B3 board into it, so I don't use expression through MIDI anymore but rather just plug the expression pedal directly.
Also, yes, all the Proteus 2000 modules share the same architecture is the same. There have been a few updates, so they need to be the same version, but otherwise, they're identical.
So...the pedal works with another setup so we know the pedal is not at fault...The only thing I can think of then id maybe your modules isn't set to the correct channels. You probably checked that already..but if memory serves, when coming from out of the box, the Proteus modules are set to the multitimbral mode. I'm going way back here, but I recall getting messed up on this. I use my E-Mu modules straight forward (I also have an X-Lead module), and I just want to plug in the MIDI and play one patch at a time, not multiple. But it was something like set up to play any of the 16 channels, and what I was seeing in the display wasn't necessarily what I was playing. This probably isn't what your problem is, but I recall having to mess with it.
I took a quick look in the Master (global) menu...There are several Realtime Controller parameters. I haven't adjusted them before so I can't say what they do...Maybe look at them?