Update... 4 months later.
After switching my internal HDD which failed (S.M.A.R.T. failure), having another of my external HDD fail (awful grinding noise), upgrading my RAM (switching first, since I had big problems with the iMac) and having to deal with a Microsoft-like acting iMac for months... after re-installing Mountain Lion from scratch a week or so ago...
I finally started using Time Machine again...
and that message appeared again!
I could notice that it's my Seagate external HDD disconnecting on it's own, while I'm working on the iMac, so it has nothing to do with it going to sleep or waking up from sleep (I also put the energy settings to "never go to sleep" and "never let the disk go to sleep"... which I'll be able to change back now...)
It also has nothing to do with the backup cycle... last time the drive disconnected about 10min before the next backup... and just now it disconnected about 30min after and 30min before... So it's not like it disconnects after x min of not working, or just before the backup...
And it re-connects after maybe 30-60sec. on it's own. I don't have to physically do anything. If I don't look fast enough, I couldn't even tell which HDD disconnected.
I had downloaded the latest Seagate HDD driver update, too... to no avail.
And according to Disk utility, the drive is ok. I do notice it's a bit more noisy than it used to be (I can hear it "thinking" a bit more louder and a bit more often, even when it should be sleeping... but it's far from loud grinding or clinking).
So that's all I can contribute. No solution, sorry.