It's either the fuse or the thermostat on the magnetron.
You can download the service manual here.
You can also find helpful exploded view diagrams and order parts by entering your full model number here: http://tinyurl.com/gv383
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William E. Miller, AS-EET
I have a different Jenn-Air built in microwave & oven combination but I'm sure my solution will work for you as well.
My microwave was plugged into an outlet located on the top of the oven. This outlet has a "circuit breaker" that tripped while we were using the self cleaning feature on the oven. You just need to reset the breaker button right next to the wall oven outlet. Why it tripped is a mystery since the microwave was not in use at the time. Bad design.
Of course, getting to the reset button is your only challenge. You need to pull the microwave and oven out of the wall/cabinetry in order to get to it. The unit is heavy so you will need help. Or, call a certified repairman and they should be able to do this for you in 30 minutes or less so the service call should not run you more than @$85 if it is no longer under warranty.
I would also suggest you contact Jenn-Air to complain about this issue and seek reimbursement from them if necessary.
I have the same problem every time I use the oven for a long time and then use the micro.
Solution is simple, yet unbelieveable.
This is a toggle switch. It is located on TOP of the oven box.
It is almost impossible to reach...but once reached, all you have to do is push it and it resets the micro.
1-remove the "frame" around the micro.
2-pull the micro out (use 2 people) far enough so that you can reach your hand - or I use a wooden yardstick- to toggle the thing. It is VERY tiny.
Xxx, there is a chance that this is on a separate breaker. Find out by plugging a lamp into the outlet and see if you have power. No...reset your breaker. Yes, take the front key panel off the unit. Locate any fuse inside. Test it with a multitester if in doubt. Also, test the thermo sensor....black, diameter of a dime, 3/8 inch thick with two wires coming out. It should be continuous. Usually, it is located on the oven wall in the keypad area. You can short the wires to test...with a paper clip...taped up...Never run without this sensor.
This advice was right on. I must have an newer model of the microwave because when I removed the front frame (4 screws) I could easily reach the breaker switch. It was on the right side and I could reach it with my hand. Once I pressed the button the microwave came on. I can't remember anything like this being this easy. Now I have to figure out how to fix the glass panel on the front of the oven door.