Recount already supports storing real-time window positions. I cannot really reproduce this problem as it does keep the windows in the saved position for me. Can you do me a favor and do three things: Can you turn off your frame-moving addons and see if they wrongly try to force the window in the wrong position? If that doesn't help delete the Recount.lua files from your WTF/* folder. If that doesn't help let me know which specific real-time window you are talking about, i.e. if its for a character or for a raid/network window.
Pardon the mess, i'm in the middle or building a new ui. Anyway, these pics were taken after I deleted the lua files from both my account folder and character folder. Notice that i'm using the smallest scale(.5) and that the lock windows option is checked. The focus of these screenshots are the Latency and FPS graph frames at the bottom. Both have been scaled and positioned in a manner that I would like them to be:
After a reloadui or logout:
What Move Anything shows:
What Visor2 shows: