Andrew,
Glad that worked for you and thanks for checking in!
The original intent of the plugin was to move all scripts to the footer (hence the name), and it was rather simple in it’s execution. I’ve expanded it since then to make it more flexible. One aspect that was a continuing theme was finding the best method for selectively placing scripts in the header – jQuery being the big one for a lot of users.
However, it should be noted, that jQuery is fairly large and not everyone wants to have it in the header. I think the checkbox on the settings page, and the corresponding filter (see the documentation) provide the best method of allowing this option while also achieving the original goal (and living up to the name). Plus, I’m using WordPress built-in methods of printing the script, which makes it work more intuitively, especially when handling scripts with dependents.
So, it’s unlikely that any future versions will be drastically different. However, as I mentioned in a previous support forum post – due to other bug fixes, some people are just now noticing that they need jQuery in the header (sounds like your case). I’m happy to hear the global jQuery option provides a solution for you and others – hopefully also making the plugin a more useful tool in many other use cases, too!
Let me know if you have any other issues!
Cheers,
Joshua