We have tweaked a future build to attempt a reconnect quickly in the event of a disconnect & only throw the mouse back to the primary if this connect does not happen with 1 second. This should help I think.
Obviously we have to throw the mouse back to the primary at some point when connections are lost because otherwise you would find your mouse was stuck on the other PC which would be a problem.
Applications which fiddle with the network sockets may well cause problems because most MP packets are time sensitive. Any delays and the mouse will start to lag on the secondary. A 0.25 second delay on sending data to a web site is unlikely to be noticed, but will be very obvious with Multiplicity.
If Multiplicity was working fine for a long period of time and then suddenly stopped working correctly then assuming Multiplicity was not updated, it seems logical to assume an outside factor is causing the problem.
Has the networking been touched in any way, have you installed a new driver, or filter driver (say a VPN). Has the firewall been updated?
Remember to include both the primary & secondary machines when you think about these things. It may be the secondary is dropping the connection rather than the primary.
Additionally, we should see if your machines have anything in common. Do you have MP or MP Pro, how many secondary pcs do you have connected, are they both on at the same time and are they both connected via wireless or wired connections, what firewalls are used, what network adapters (if its nvidia then please turn off any 'offloading' features it has).
A large number of machines at Stardock are running Multiplicity and I do all my vista development via it without any problems, so its not a case of Multiplicity is inherently unreliable. Something is causing the network connections to drop. Either Multiplicity is dropping it because the 'are you alive check' fails (not sure if synergy has one of those), or because the network stack has detected a problem and has dropped the connection.