Linux window position saving

I'm noticing a bug on Linux (Xubuntu 14.04) where the window position adjusts between application closing / opening.

Here is window.json opening and closing 4 times:

{"maximized":false,"position":[258,136],"size":[1000,850]}
{"maximized":false,"position":[259,160],"size":[1000,850]}
{"maximized":false,"position":[260,184],"size":[1000,850]}
{"maximized":false,"position":[261,208],"size":[1000,850]}

Every time the window is closed it adjusts x by x + 1 and y by y + 24.

Not seeing this behavior on Windows. Wonder if this is an xfce thing, an atom-shell thing, all Linux? Who knows.

Might also have to do with the way we're closing the window right now using destroy() instead of following normal window close lifecycle.