Could you please provide me a copy of the script you're using?
I know that Inquisit doesn't contain any code that would set it to double pulse mode (a13). However, if a response box is used as a stimulus via the <xid> element we do set the lines to General Purpose (a10), the direction to output (a4), and optionally set the pulse duration (ap). I haven't confirmed, but we may also set that if you just have an <xid> element in the script, but that would be an easily fixable bug.
If you just have a single XID device used just as an input device (and you don't need to scan for a specific one or alter the pulse duration) you can just specify /inputdevice = xid in <defaults> and omit the <xid> element and Inquisit shouldn't touch those settings.