Brushes are sort of a special case when it comes to hotkey assignment. The main modifier keys Shift, Ctrl, and Alt all have hard-coded functions related to Brush behavior, and may conflict with or break hotkey assignment. Alt is the safest to use with brushes and some quick tests here indicate no problems using it, but it would be my guess you have a problematic combination somewhere that breaks your hotkeys when you attempt to use it.
With brushes, I recommend following the documentation for Brush hotkey assignment and select them with the customizable letter combos from the Pop-up, or creating a custom pop up panel with a limited situational selection of brushes, and assigning the hotkeys to that panel rather than the brush.
This I have no explanation for. Understand that the above is only a guess based on general experience. This might indicate some sort of hardware conflict. If you’d like to work through an issue in a more technical fashion, you would need to contact Pixologic Support and start a conversation there. You would need to provide them with more specific information about your installation and usage.