Well donncha, I followed your advice and upgraded to WordPress 3.0, which was a huge drama considering all the ancient plug-ins my blog depends on (and an out of date theme as well). Fortunately most of them work fine (and those that didn't had more modern equivalents), so in spite of all the work I'm happy with the results.
Anyway, regarding Super Cache, the good news is that the PHP errors went away as you said they would. But like Fabian, my cache preload still gets stuck between 100-200 posts. In 2.6, it didn't actually cache anything at all, whereas it does cache some posts now (but far less than 100). Worst of all though, I couldn't cancel it - the "cancel cache preload" button never goes away, no matter how many times I tried to stop it.
I ended up having to deactivate Super Cache and clearing its options from the database - it seems to me that the cache preload functionality is seriously broken right now.