I set custom keyboard shorctuts to "W" + "E" (W=move frame forward, E=eraser).
However sometimes they don't work and 50% of the time the shorcuts bring up either the "Window" (when I press W) or "Edit" (when I press E) menu. I've searched and searched but can't seem to find a solution.
Im on a Windows 10 machine with a Cintiq 24"
That would happen only when you press ALT first - it activates the menu bar.
Since you're on a Cintiq, also make sure you disable Windows Ink both in your Wacom driver and Animate's Preferences (Switch to WinTab).