So I tried the upgrade to hardy, and had this happen (noted above).
Today I got fed up with it finally, and just decided to do a completely
fresh install with no cruft leftovers.  ARGH!  Nope, it's still
happening, but at least not as often.  As I try to think through the
logic of what is happening, it has to have something to due with it's
initial switching to the other screen.  Perhaps it's a clipboard sort of
problem?  Has there been major changes to the clipboard functionality in
hardy?  There's not really, from what I can tell, a pattern of
reproducibility either, as sometimes you switch from screen to screen
back and forth quickly with no problems, then randomly it lags.  There
also might be something to how long it's been since you last switched,
as if you switch quickly it works for a while, then just lags then comes
back after about 5-10 seconds.  Additionally there appear to be zero
performance issues as far as cpu or network bursts.

So frustrating, but I'm sure some genius will find the problem soon
enough:)  I will buy you a sixer of beer if you do it.  Seriously.  I so
miss this (critical) package.

FYI: this was downloading alpha6 from the official release site
(03-13-08), applying all updates to the system, and then installing
synergy.  I would also say that there's not really a time limit to when
it happens, just randomly, even after you've used the desktop a bit,
moved around etc, typed, (maybe even pasted).

-- 
[Hardy A6] Input freezing when using Synergy
https://bugs.launchpad.net/bugs/201041
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