Logos has had this issue for a while - for me, at least... windows that are full-screen (whether "zoomed', that is "maximized" to full-screen or resized to full-screen by dragging the resize handle at the bottom right) invariably show up tiny in the bottom left of the screen after restarting Logos. See below for a sample.

Interestingly enough this doesn't happen with windows that are big, but not quite full-screen. I'm running Snow Leopard 10.6.5 on a 17" Macbook Pro at 1920x1200 with the latest beta - that is, 4.2a Beta 3 (4.21.4.8572).
Anyone have a workaround I might try?