So, 2 of 3 coordinates are recorded: position-within-monitor and size.
The monitor-number is not yet recorded, nor is its absence or presence detected on startup, so if the display resolution of a 2nd monitor is different from the primary monitor when the 'Save Window Size" command is executed on the 2nd monitor, the position and size undergo an (unintended) translation the next time OmniWeb is launched.
If the use of a 2nd monitor were a new feature that OmniWeb had to catch-up with, I would consider it to be a needed enhancement.
As the use of a 2nd monitor has been a standard part of Mac OS X for a long-time, I consider this to be a bug.
The absence or presence of secondary monitors should be a standard part of the Quality Assurance testing scripts for all of your products.
Otherwise, great products. Just my two-cents worth. Thanks.