In QuickBooks under the Window->Workspace menu do you have AutoSave checked? If you do it is supposed to remember the position and size of windows. I tried with a check register window and it is working for me.
Which register are you saving? (There are several different types)
The auto save information is using Apple's mechanism for autosave. The position data gets placed in the QuickBooks preference file. You may have a corrupt preference file - in that case try quitting QB and deleting your preference file. To delete the pref file do this:
1. Quit QuickBooks if it is running.
2. In the finder hold down the option key and click on Go->Library
3. In the Library window that opens double click on Preferences
4. Drag ALL files of the form com.intuit.quickbooksxxxx.plist to the trash (where xxxx is a year, like 2014 and 2013). Make sure you only delete these plists and make sure you get all of them.
5. Relaunch QuickBooks
