Looks like 9.0.3 fixed it.

Mac 10.5.8
Tranzport 1.00
TM 1.4.2
iTunes 9.0.2
Logic 9.0.2

I've been using the Tranzport to control iTunes from the drum kit etc, but now it disappears from Menu Bar when I select iTunes Controller, the screen goes blank.
I have not added/updated or changed anything lately, so this is strange.
I tried new batteries twice.

I also have an Alphatrack connected for controlling Logic 9.