Thank you all so much, scottiesmum's suggestion cured the problem, easy when you know how , but I still don't know what I did to cause it.
Internet Explorer will remember the size of the last window to be closed, and open any new windows that size accordingly. If you simply maximise the window it doesn't remember that, and only remembers the size of the un-maximised window.
This is a double-edged sword, as yes, it's nice that it remembers what size you like your browsing window, BUT if the last window to be closed happens to be say a small popup window (which lots of download sites seem to open for a file download, in order to get around the Information Bar popping up), then IE will remember this as "your IE window preference", which of course is nonsense!!
Easily fixed by following Kate's advice though - open a single IE window, resize it to how you want (NOT maximised!), then close it. Next time you start IE, it will be the same size as you left it.