It might be fixed.
I have not had the problem since 10.9.2.
Note that I can't guarantee that the update fixed it for me, as my system drive was corrupted right after updating to 10.9.2 when I tried to troubleshoot Finder lag (10sec hangs when browsing folders). So, I wiped the drive, started from scratch with a clean install of 10.9 from a thumbdrive and then onto 10.9.2.
So, for me on a clean install with 10.9, upgrade to 10.9.2 and the same apps running, I have not seen the anomaly.
No not fixed. My iMac with second monitor still has all the apps open in weird positions and sizes, off screen. Some of them I cant resize they jump back offscreen, have to close and reopen them. So thats still happening to me. Amazing how long this issue has been happening and Apple not fixed it yet.