I've had this problem ever since I installed Lion last year (and it persists after the upgrade to ML). It's conceivable that the problem occurs specifically when you install Lion over the top of Snow Leopard. (I cannot confirm this, but it's what I did.) This also includes setting up a new machine from my TM backup where the original machine made the Snow Leopard->Lion transition.
The guy at the Apple store suggested a full clean reinstall, but there's absolutely no way I'm spending hours and perhaps days reconfiguring everything the way I want it (terminal scripts, aliases, colour profiles, BTT settings etc etc). No chance.
I do not and have never had Sophos.
Of interest: if you set your TM backup volume to be a conventional HD rather than a time capsule (or perhaps any network drive?) the problem does not occur. So it is definitely time machine related. (This also tallies with the fact that the popup comes every hour, exactly; interestingly it always comes in a pair, i.e. after I dismiss the first popup I'll get the second a few seconds afterwards.)
I haven't tried setting both the Time Capsule and another drive as joint backup destinations; maybe that would work.