Comment 11 for bug 1303462

the best workaround I have come up with is:
- install compizconfig-settings-manager from the software center
- run compizconfig-settings-manager
- go to place windows
- go to fix windows placement tab
- create new (windows with fixed positions)
- window postion: class= "the program that is loading in the wrong position"
- X=65
- Y=55
then close
 repeat as needed for all program causing problems and adjust X & Y based on you launcher and panel scaling.
some time you have to restart for the setting to take effect.

hope this helps
cheers!
Whitaar