i don't know if ye've the same problem as me, but we've been having some real slowdown issues in the last few weeks, especially when we go to the post-new.php page.
so i tracked it down that WP Super Cache was trying to delete all autodraft posts (over 7 days) in the background. in this it does a purge on all the supercache files in wp-content/supercache folder ... so it was iterating through all the folders in there. not good for us because there was roughly 2500 folders in there, and it was taking about 8 seconds. for some reason it was doing this twice, but that didn't bother me too much.
the matter was made much worse when it decided to delete multiple drafts at the same time (sometimes up to 20 or more), which was a delay of 20 * 16 seconds ... which is usually a timeout ... as the RAM etc on the server goes mental.
end of the day, i deleted the cache (in the supercache settings pages), and everything sped up, but i guess i'll have to be doing that kind of often now until the problems are fixed.
but it would be good if wpsupercache cleaned up the folders after itself when it was deleting expired supercache files. that would solve some of the problems ...