Same problem here. I updated to 0.9.9.9 and wp 3.1 and the code that uses the “dynamic-cached-content” tag, that worked previously with 0.9.9.8 and wp 3.0.x, is now returning blank pages with just wpsc’s timestamp on them.
Also, it does not allow me to delete these blank cached pages manually from the cache list (unless I delete the whole cache).
Note: something funny seems to happen with $wp_super_cache_late_init. After setting it to 1 and uploading the wp-cache-config.php file, it seems to reset it to 0 by itself after some time.
In any case, I re-tested it while the $wp_super_cache_late_init was set to 1 and it still returns the blank page with the timestamp, and does NOT return the phrase “Super Cache dynamic page detected but $wp_super_cache_late_init not set.”