Actually, I jumped the gun too soon I found out after more testing today. Elements are being prepended fine--the MS debugger is giving a false error. Instead, what's happening is IE doesn't like my ajaxStop call for whatever reason (well, it's likely a race condition that IE stumbles over but other browsers handle, but still a race condition that needs fixing). So now I'm off to debug that. Again, the culprit is more likely my code not jQuery.
-jody