When using multiple displays, switching between activating each display may cause Amphetamine's system menubar icon to lose its low-opacity. This due to the image in the menu icon draws over itself multiple times.
1) Deselect low-opacity icon option in Amphetamine's Style preferences
2) Navigate to → System Preferences → Mission Control → uncheck "Displays have separate spaces"
Note: A code-fix to address this issue is being researched/investigated.