I've been having the same problem for a couple versions now, but nobody seems to notice or care, no matter where I report it. And I am running the newest version, on a clean install of Windows 2000. Nothing helps.
One other thing I've noticed is that when you mention 'query logs' people seem to automatically assume that you mean the contemporaenous/'real time' logging toggle. IT'S NOT THE SAME THING, PEOPLE!
We're talking about Buffer-->Save As.. okay? Be clear on that!
At first I thought it was maybe just a problem with saving query logs across the network, but it happens on local drives too. But even if it had been only affecting network saves, it needed to be fixed. Some kind of "query logs do not save across the network" disclaimer would not be appropriate. If it doesn't work, then don't include the Network Places option in the query save pop-up!