We may be thinking of a different issue then, because when my window disappears, no amount of reloading helps. Also if you set the window position using MoveAnything, I think it remembers, so you don't need to do it every time.
I had a similar problem with professions not opening . . . apparently.
What was actually happening (and I did not even have NPCScan installed, so it could not be responsible, as such), was that the window was opening, but off-screen. I could hearit opening and closing, but it never appeared.
To fix this, I used the MoveAnything addon. Using this, I was able to "reset" the window, which made it visible for me.
I suspect that it was a library that came with one of my other addons that caused the issue. It may be the same here.
For anyone wanting to try this method, once the MoveAnything addon is installed and the game is running:
Open MoveAnything from the Game Menu (press the Esc key enough and it will appear).
Find and open Info Panels in the list.
Find Trade Skills in the sub-list (NOT just Trade).
Click the first tick-box (Mover).
Click the Reset button, or move the window to any location you like.
Hopefully this will help people seeing this issue until a better fix becomes available.