I had this problem. I turned on email notfications and got this:
The WP Super Cache Garbage Collector has now run, deleting 0 files and directories.
The following warnings were generated by the WP Super Cache Garbage Collector:
Cache expiry cron job failed. Job will run again in 10 seconds.
Then I saw that I had preload mode set to "on" but "custom_preload_interval" was set to 0 (as in zero seconds, or turned off). I turned preload mode off (unchecked the box) and files stated to get deleted again. Now the notification mails look like this:
The WP Super Cache Garbage Collector has now run, deleting 174 files and directories.
A better handling of this would be nice. Like the first mail telling me it did not delete anything because of the preload settings.