Hello!
I've tried (with no success) to replicate the issue with the mouse pointer on my test project. However, I've just released version 1.1.0 adding a forced update to the "hide status", and the option to add a "mouse down" pattern for any cursor pattern. Just add a new pattern, and reference it on the new parameter for the main one.
Additionaly, you can also trigger the mouse pointer to be shown or hidden with plugin /script commands. For MV users, use the plugin command "MousePointer hide|show". As for MZ users, use the "Mouse Pointer State" command. On both engines you can also use the script commands $gameSystem.showMousePointer() and $gameSystem.hideMousePointer().
Hope this helps! =D