I am having similar problems.
Mac mini '12 16GB 256SSD
24" display 1920x1200 + menubar + arranged right, HDMI (main screen)
19" display 1440x900 rotated 90deg (portrait) + arranged left, TB to DVI (side screen to review online data, text documents pdf files, ...)
Sometimes randomly the login will appear on either screen.
Equally randomly one or both screen will flicker on/off during startup and then one of the screens may remain black, typically the login one, rather than have the colored background
Most annoyingly every time my system wakes from sleep, every program window on the 24" screen is narrowed to 900px wide (as if to fit the 19" portrait screen) and in my opinion worse, almost every application window is moved about 240px down from the top menu bar, as to align with the horizontal bottom of the 19" portrait screen. ( 240px diff between 1200 & 1440) So several times a day I'm resizing and rearranging my app windows.
Also seemingly random, I can be in the Finder, Safari, pick any app. Through whatever action there will be a popup or confirmation dialog; and even though I"m on the 24" screen ... that extra dialog comes to the side screen! Last one was emptying the trash, bottom right of 24" screen ... confirmation popup centered on the 19" screen ... two feet over to the left!
Can't do a full screen with menu bar?
If I do one app like open office or libre office full screen, then when I switch to Safari or Finder to look up text or a document, poof my full screen office app disappears ... as if I'm not allowed to have two things going at once. I can only bypass it by manually maximizing apps on both screens.
I've also had major problems with apps not properly resizing to a smaller screen. They seem to exist in a virtual large screen. So if you try to push something from the 24" to the 19", it will remain at whatever size I had it on the large screen, without any access to the resize handle.
It really makes me wonder sometimes what Apple is doing to have these functional regressions and/or bugs.
The screen shot from AppleG33k above, does give me a hint try to realign the portrait one vertically higher. Both my screens are physically top aligned, so I have it factual in arrangement, ... but maybe cheating that may help with the vertical repositioning until Apple fixes this.