Ok.  Deleting the plist files is not a normal operation - its a tech support move.  We are trying things because the problem is not one normally encountered. The window save position is stored in the plist so wiping that out might help if there was something corrupt in that preference file.

The Window position saving is part of the Apple window APIs for the most part (there is special processing in QB for some of them, like the toolbar).  In the plist each window has one that looks something like this:
NSWindow Frame 3D81DED3-573D-44D0-ACF6-92F1BA047D14_HomePageWindowFrame 996 564 1016 636 0 0 3008 1669

The numbers following the "frame" part are related to the window position.  This comes from Apple's APIs - I'm not sure how the numbers are interpreted by the Window manager (though I probably could look it up).

Anyway, something is wrong, and yours aren't being saved.  We did recently find a bug in the handling of the writing of the prefs in some theoretical instances - we've never actually encountered it.  A fix for that should be in the next update.  It _might_ have something to do with what you are seeing.  

I don't know what version you are coming from. Performance should be better in 2016 than 2015 but there is a wide variance in data in different companies files and that can effect performance.  Try running File->Utilities->Rebuild.

There are a large number of new features in 2016 if you are running Sierra. <a rel="nofollow" target="_blank" href="http://www.qblittlesquare.com/2016/09/whats-new-quickbooks-mac-2016-r6/">http://www.qblittlesquare.c...>