I'm wondering why you feel the need to turn off your sub in the first place, which, if I've read your post correctly, appears to be the source of your problem. As the EP-125 has auto-sensing circuitry, why turn it off at all? After a period of time in which your sub is not sent a signal from the receiver or pre-amp (i.e. around 20 minutes, and you've been listening to music in two-channels, speakers set to large), the sub will go to sleep, or power down, and won't make a peep until it receives the next signal, as in the next time you're watching a DVD in a 5.1, 6.1 or 7.1 format, or using a multi-channel audio format (DVD-A, or SACD). I've owned an EP-175 for about two and a half years now and I never turn it off, though it is often in an inactive state, awaiting the next signal, and I experience none of the difficulties you describe.
My apologies if I've misunderstood your post, and best of luck, sir. Cheers!

DS.