So I've seen this issue on here several times and the answer always comes back to checking the "Print Blank Printer Spreads" option in the "Print Booklet" dialogue. Well I've checked that and it's still doing it. It's adding two pages in the same places (pages 1 & 4) in every booklet project I have. I've tried resetting the preferences and that did nothing.
How many pages are in your document?
I realised after posting this that it was due to the number of pages in the document not being divisible by four. This has resolved the issue. Big facepalm for me...