I'd leave a station in a large ship, boost straight away from the toast rack - I thought that was the quickest way to get out of mass lock - only when I'd cleared mass lock would I engage jump drive, line up perfectly with my jump target - then wonder why I was getting the 'Align with Target' message.
I've only just realised that it doesn't matter how perfectly you're aligned with the target system: the game won't consider you to be properly aligned till you stop drifting - and big ships do a lot of drifting.
Now, if I'm in a large ship, I boost turn onto my target system heading as soon as I get clear of the toast rack, so that I've stopped drifting by the time I'm clear of mass lock and can jump without waiting for the drift to stop.