I suspect that the Zumo 32U4 might have been accidentally programmed as an Arduino Yun, which would explain why the Zumo is being recognized as an Arduino Yun instead of an A-Star 32U4. We have seen that issue before with an Arduino Leonardo, which we do mention under the "Programming using the Arduino IDE" section of the Zumo 32U4 Robot User's Guide, but not an Arduino Yun. Regardless, the Zumo should work fine when programmed as an Arduino Yun (or Arduino Leonardo).
To get the Zumo to be recognized correctly, you would need to reprogram it as an A-Star 32U4 by selecting "Pololu A-Star 32U4" in the Tools->Board menu of your Arduino IDE. However, since the A-Star 32U4 board entry is missing from list, can you try re-installing the text files we provide to add that board entry to your Arduino IDE? (If you are not sure, see step 2 under the "Programming using the Arduino IDE" section of the user's guide. Please note that you might have to restart the IDE.)
If the problem still persists, can you post a screenshot of your "hardware" folder under your Arduino IDE's sketchbook directory?