Apologies if any (or even all) of these have been reported before.
1) Customized keyboard shortcut for Build command not honoured
To reproduce, remove F5 from the RUN command and assign it to the Build command. The accelerator shortcut shown in the Build dropdown menu is still F7, and hitting F5 does nothing.
2) Build And Run shortcut not customizable
I think this was a new command added in recent versions? In any case, it does not show up in the commands list in the keyboard customization window.
Also I've noticed in some places the commands are referred to as "Build" and in others (e.g. assembler toolbar tooltop_ as "Assemble". Is there any difference, or reasons why the naming isn't consistent?
3) Menus don't capture keyboard input
a) Click anywhere in the code window
b) Press ALT+F
c) Attempt to use the arrow keys to navigate through the menus and press enter to select one. You'll see that instead, your keyboard strokes go into the code window.
To see how it SHOULD work:
d) Ensure the IO toolbar is visible
e) Click the whitespace in the I/O View window
f) Repeat step c from above. If the focus is not in the text editor it works properly.
4) I've noticed several other GUI-related bugs in the product (e.g. some C keywords not highlighting, menu commands mysteriously becoming disabled for no good reason, window focus issues when hitting the Run button, etc) and will provide more details if I notice patterns that reproduce them. The tool seems to have promise as a nice, simple AVR development environment, but these GUI/IDE issues are taking all the hard work that went into it and making the product feel sort of half baked..
Hope the feedback helps!