Well, after doing a few compact-and-repairs, closing and reopening etc, the problem (this particular one) has gone away, and this particular database is no longer giving me any problems. I will keep an eye on it and the next time it happens rather than trying to fix it I will send it off to you.
For what it's worth, this is one of the web pages that caused (or seemed to cause) this problem:
http://whatscotlandthinks.org/questi...ication-5#line
One of the features of the problem is that at some point, eg after compact/repair, UR will tell me this page has changed, and do I want to save the changes (this is even if I've saved it as a link in UR, not stored). UR will then create a folder containing all the .js, .css .svg etc files for that page.