The alt-tab freeze has been an age-old issue for as long as I can remember (at the very least since 2007; and yes, it is incredibly annoying when it happens. You have to "End Task" Windower from the Task Manager just to close it once it freezes). I remember there were a few bug reports on it in the past, but none of the Windower devs could ever pinpoint the issue, as some people had the issue while the majority didn't.
About a year ago, a friend of mine was able to figure out that it had something to do with having a gamepad connected while using Windower and the freeze would randomly occur whenever the game window processed the focus/unfocus events (ie: alt-tab). Since the freeze is so unpredictable, you can't really "reproduce" it on command, so he went as far as to make an application to spam alt-tab 50 times per second while he was trying to figure out the cause (he would get the freeze within seconds from this). At one point, he tried disconnecting his PS2 gamepad from his PC and after running his little application for 30 minutes he could no longer reproduce the issue.
I don't think he ever formally submitted the bug report on it though, so if any of that information helps on resolving the issue, that would be great!
Just wild speculation, but the official FFXI Window mode was added sometime around the 2007-2008 time frame as well; if you've ever tried it, you'd notice that the gamepad takes a good 2-3 seconds to "rehook" to the game after leaving and re-entering window focus (gamepad is completely unresponsive). Could the alt-tab freeze and Windower have something to do with this?