Thanks Shoggy, but that isn't the issue. I very rarely minimise the window.
To recap: on attempting to open Aquasuite normally, it appears (this happens very quickly) to try to open 2 windows (within the 1 Aquasuite main window, the one with the logo). All then disappears. Aquasuite will now appear in system tray and can only be opened here. It appears that Aquasuite is attempting to open 2 databases?
Very confusing.
Solved!!!!! I am a complete numpty!
START MINIMISED was checked in the EXTRAS item in the Aquasuite menu. Duhhhh!
Thanks Shoggy & Seb for your patience.