A very nasty problem - AI modders please help!

[Rexxx]

My guess is that the problem comes from the different weapons.
It could be that the AI takes the torpedo (which you have in your battlecruiser and as second pick in the DN without QR) as the "better" weapon. For the AI (at least sometimes) a weapon is better if it researched later.
Happens to me with missiles/PPB and switching between small and medium weapon platforms.
Have you tried equipping the DN with QR qith a torpedo or using it as a second pick? Another possibility might be the alteration of your research file. Make sure that the hellbore is researched after the torpedoes.
Hope this helps.