Hi FW,
As you suspected, the reason why the sync will stop when particular QuickBooks windows are open is because the QuickBooks SDK prevents any requests from being made while these windows are open. As a general overview, having a specific Entity/Transaction open will prevent modification from being made, as well as any Preferences/ settings window.
For a complete list, this question would be better directed at Intuits Developer team, as the Add/Mod lock is the same across the board, and is not specific to Method. If you were wanting to test which windows will prevent sync from occuring without having to make modifications to method to test every time, you could look into using the SDKPLUSTEST3 tool from Intuit. This tool allows you to parse xml requets directly into the SDK, bypassing method.
Thanks FW
Regards,
Ben