Incompatibility issue with PuttyCS

I'm a huge fan of Multiplicity Pro, and I've been a user for several months now. Recently I've rebuilt my work destop to use Multiplicity as well. As a sysadmin, I frequently use PuttyCS (Putty Command Sender) to carry out identical one-time operations on large clusters of servers. Unfortunately, when I try to use PuttyCS on a host that is a Multiplicity secondary, the behavior of PuttyCS becomes erratic. Some putty terminals are ignored, while others receive double input. Sometimes linebreaks are totally dropped to all windows.

These things do not happen if input comes directly from a locally attached keyboard, with Multiplicity unloaded. Unfortunately, it's impractical for me to use this machine as a primary, as it is a notebook which is frequently undocked and taken elsewhere, and it is the only system in my workplace authorized on the VPNs to which I need to connect, so running these commands from the primary host is also not an option.

As much as I like Multiplicity, this is a real dealbreaker. PuttyCS saves me hours of time every week, and I can't work without it. If I can't get this resolved, I'll have to give up on Multiplicity. Please help!