Hey, thanks for the feedback and glad you enjoy the plugin.
At the moment, I'm not aware of any workaround for the issue. The shortcode function uses Regular Expressions (code inside of code in a sense), and its gonna need a detailed inspection and then redesigning to get all the dings out of it. There's other issues that have surfaced related to the one you had just explained. So it is a project that I plan doing in the future. Unfortunately, not on the current project.
In the mean time. Keep an eye out for the new update. I'm currently working on adding the 'custom post types' and the 'custom taxonomies' feature to the plugin. So don't get too carried away with the default categories (just a heads up)...and sorry about the issue, there isn't much I can do with it til a later date X(