When I open ToME, the window places itself so the top and left edges are just off screen, title bar included. Dragging a visible edge to resize the window reveals just enough of the title bar to let me drag it towards centre screen - but it moves back the next time I start the game. This sounds like a minor thing, but it's getting annoying.
This "bug" does not cut off any of the game pixels, furthermore, you can move the window by pressing ctrl+space and selecting the move function.
You could center it every time you play, or do what I did and make it roughly half the screen like when you drag a program all the way to the right/left.
Oh also, don't launch Tome from the taskbar, it does not like that.
What I do is Alt+space, m (shortcut for the Move option), hit an arrow key, then use the mouse to position the window. For some reason the window won't follow the mouse until it has at least one keyboard-based move first.
Oops, you're right its alt+space, my bad. Moving every launch is annoying so I just got used to the idea of playing with the game being in the top-left corner and using my entire left side of the screen. Roughly 50-60% of the width of my screen and about 95% of the height (I auto-hide the toolbar but leave some space to access it when needed).
*I mentioned the taskbar thing because if you try launching the shortcut from the taskbar for whatever reason the game will randomly (majority of the time) have issues like: Not running, blank window, no sound or music even when enabled.
One of my other annoyances are the tooltips, which while incredibly useful, tend to block other, vital information that I want to see when I'm playing the game. The new interface looks like it was built with such concerns in mind.