I just wiped .htaccess clean and re-installed the plugin. The behaviour I get is as follows:
Only the top bar of the Dashboard appears after activation. If I click out to Visit Site, then click Site Admin, I get a 500 Site Error.
It could be, presumably, that Super Cache doesn't play nicely with the other plugins I have - these are as follows:
Akismet
Amazon Machine Tags
Bad Behavior
Easy Tube
Google XML Sitemaps
Simple:Press Forum
SimplePie Core
SociBook
Ultimate Google Analytics
WordPress.com Stats
WP-o-Matic
However, removing Super Cache eliminates all problems with the functioning of the site - just it's a bit slower. Super Cache did work for me, with all these plugins and the previous version of WordPress and Super Cache: its operation, however, was somewhat cranky.