This might be an issue with your actual setup - have you looked into handy programs like DisplayFusion or ActualMultipleMonitors that remember window positions?
Here on Windows 8 i have no problems with the b4a IDE window remembering it's position - i have 3 monitors and it alwasy remembers it's last position.
Try positioning the IDE window where you want it ensuring that the window is not maximised, now close the IDE and reopen it.
Does it not open at the last position?
When the settings are loaded the negative position is ignored. The purpose of this check is to avoid cases where the position is no longer visible. It can be improved in the future...