I was adding it via getBot().addMouseListener(mouseListener); directly. I changed it to how you do it and it now works until I open the logger, then everything goes to hell.
Just tested quickly:
Disable input worked initially
After opening logger disable input no longer works
Mouse listener did not work at all (my scripts use this a lot, hoping for a fix).
edit: mouse listener partially works in .127, not at all now.
To confirm what others have said. If I open a new client and start a script disable input doesn't work at all. The game is getting all of my inputs. Also, mouse listeners do not work at all in this version whereas they mostly work in the previous version.
I wonder if this is related to the changes that happened recently to how the canvas is displayed.