Yes, you're right and I initially thought that too but it's not just the one pair of headphones - the headphone jack essentially seems to have failed on both computers. No device is working on either computer now.
The only thing Multiplicity could ever do is alter the jack detection and it will have only have asked about that if no output devices were detected. It would also require you to confirm it as it is a prompt and it would have only have even checked that on the capture end and so not both computers anyway.
If that is the case it can be undone with a registry edit, but it shouldn't stop a port working, purely make it always think something is plugged in so as to not be muted always.
An easy way to tell is to look for the following registry keys using regedit
There is a key called EnableDynamicDevices which would default to 1 (or possibly not existing at all)
There is a key called ForceDisableJD which would default to 0 (or again possibly not existing at all)
If those are not those values then you can set them to be that and reboot.
Or actually an easier way would be to go to Multiplicity audio, click advanced settings and untick the Disable Windows 7/8 jack detection if it is ticked as MP would then adjust that setting for you
Also remember whilst MP is set to share audio you will get no audio from the sending machine locally, only on the computer it is being sent to.