There are many bugs I've spotted with alt-tab and alt-backtick; I'll try to compile a list of unit tests for you as soon as I have more spare time. Here's one to start:
1) Open 3 windows of the same application (e.g. Terminal). Make sure each window has different content so you'll be able to tell them apart. Let's call these windows A, B, and C, from top to bottom.
2) While holding down Alt, hit ` twice.
Expected result: window C is now on the top of the stack. The order of the windows is now C, A, B.
Actual result: window A is still on the top of the stack. The order of the windows is still A, B, C.