That is indeed the main argument against using Tor and Not using Tor at the same time. It primarily applies if you are surfing to the same website with both of the connections simultaneously. For example if you are in an IRC channel using Tor with one nym and without using Tor for another nym, if your internet dies both of the accounts will ping timeout at the same time. Maybe you idle and someone DOS'es you a bunch of times looking for a consistent pattern.