Desktop Arrangement Wrong

I have two Thunderbolt displays. One is plugged into the Mac Pro, and the second display is plugged into the first display monitor.

It goes like this:

Mac Pro <— Primary Display <— Secondary Display

As of now, the displays have consecutively provided the wrong arrangement. The Primary Display and Secondary Displays switch places.

The answer should be rearranging them in the Display options, in System Preferences.

Unfortunately, it thinks the setup is still the same as it is before. Trying to rearrange them does nothing, in fact. It insists on retaining the same setup.

SMC and PRAM resets haven't helped either.

There is a temporary solution in unplugging the Secondary Display from the Primary Display, which then finally returns the desktop to the Primary.

Also, there is a rare chance that the arrangement will show up correctly when booting up or plugging in the Secondary Display.

This isn't the only unusual circumstance of my Thunderbolt display: upon booting up the Mac Pro, the Secondary Display will sometimes (rarely) decide to not power on at all.

I've had these displays, and Mac Pro, since early last year.

Any help would be much appreciated!