Upon updating from 0.8 to 0.8.1 my 3 existing CPT's (created with this plugin) permalinks broke (resulting in 404s). Flushing the permalinks did not resolve the issue.
The "with_front" option had produced problems in the past, so I went back into each of my CPT's and reset each "with_front" option (each were set to "false"), but had no luck. I also tried switching each to "true", also with no luck. Regardless of which option I selected, the behavior remained the same: the "base" was being prepended to the permalink, causing an improper URL.
I decided to use the "Get Code" link on each CPT and compare it to the WP Codex for accuracy, specifically the "with_front" value. Sure enough, each CPT had a different value for "with_front" (which requires a Boolean): "1", "true", and "0" respectively. My CPTs were set to "false", "true", and "false" respectively in the plugin.
I used the code to manually create the CPTs in my functions.php file, corrected the "with_front" values to "false", "false", "false" respectively, disabled the plugin, flushed the permalinks, and everything worked again.
Hopefully this issue will be resolved soon, as this is a great plugin.