Thanks everyone.
Firstly, I checked some (not all because...time) of the slow ePubs. None of them threw any scary errors (mostly they seemed to be innocuous HTML anomalies which as a web developer I wouldn't worry
too much on a page) e.g.
Code:
Error while parsing file 'attribute "prefix" not allowed here; expected attribute "id"'.
Error while parsing file 'element "hr" not allowed here;
Error while parsing file 'element "tr" incomplete; expected element "td" or "th"'.
etc (I'm not even sure where the tables are in that particular epub).
Anyway, based on the other suggestions I've determined that my version is Marvin 3.1 build 32
I also cleared the cache, which was 45.7Mb (I don't know if that's a lot or not).
After clearing the cache, I tried one of the offending files again and I don't know whether I was imagining it or not, but it seemed quicker.
If I get any slowness again, I'll tag the file (so I remember which one to check later).
thanks everyone!