Great work on Super Cache. I am the maintainer of Advertising Manager, another WP plugin. I was researching a bug today, which was caused by WP Super Cache being enabled.
Basically, changing any ad settings by the administrator was not being recorded to the database, and thus the widgets were not displaying correctly.
I saw that your cache can be turned on/off for logged in users, etc. Is it possible that your cache can be ALWAYS turned off if the user is_admin()? This way, any work that will most likely affect the database can proceed.
If you have any other solutions, I would be grateful to hear.