Possible issue when disabling with_front on CPT

I have my permalinks setting as:
/blog/%postname%/

I have some custom post types and I have with_front set to disabled. When I use this plugin it seems to override the with_front option being disabled and causes issues.

For example when this plugin is enabled the CPT archive goes from:
/cpt/
to
/blog/cpt/

Any help would be great.