Ahh thanks guys, I could have sworn that the other cars I tried were set to "ACC" and were still allowing me to use the windows, but it must have been when they were set to "ON", as I just went out to test the windows again on my Skyline then and it worked exactly as described - windows working when engine off, but set to "ON".
Sorry about the confusion there, but thanks for the help!
Hehe this is one thing I've appreciated about the turbo timer, a few times already I've been driving around with the windows rolled down, stopped somewhere and taken the keys from the ignition only to realise the windows were still down... but thankfully with the engine still running for a brief period it is just enough to get them back up before it cuts out!