This is what I think is the problem with the way Applebee's times orders:

The way courses are timed at most dining chains is that either a)app and entree are entered into the computer at the SAME time, and the computer does not "release" the entree to the kitchen until the app is completed. OR b) the two courses are ordered separately, in which case the server doesn't enter the entree order until they see the app has been delivered to the table.
This allows the table to be enjoying their app while the entrees are being COOKED. Any place I've ever worked cooks food on the grill/sautee/etc.
HOWEVER, from what I understand, Applebees gets most of their food already "prepared" and is then finished in the microwave. This cuts way down on cook time, and causes the two courses to come too close together or at the same time.

It's just my theory, but it makes sense. I always just thought the whole microwave thing was gross, but now I'm seeing another problem with it. They seriously need to add 5-10 minutes to their computer and/or manual timing if they want to remedy this problem.