You might actually have found a bug, either in the compiler, or in your MCU, or possibly in your own hardware implementation. I'm always a bit nervous when someone is using an ATMEL product.

In any case, a bit of work with 'scope and logic analyzer will show you considerably more than you're likely to want to know. You might even want to compare the signals with and without the emulator. That will, perhaps, show you things you certainly don't want to know, as you'll then have to deal with 'em.

RE