- turn off the mod, see if it is responsible.
- see if the autoattack is turned on - indicated by a spinning something animation on the attack button in the control panel.
- make sure the enemy ships are not magically dying. SoaSE is set to automatically cut flashy effects to save memory for calculations; the attacks are still happening, but the pew-pew is not seen.
- make sure the enemy is not using something nasty on your ships. I can't recall anything that might turn off weapons of a whole HC group, but maybe the mod has something like it included?
- are you sure you're attacking the enemy? Maybe it's an ally, maybe you accepted a peace pact?
- maybe an Akkan used its ultimate skill?
- maybe you're attacking a Trascencia starbase that used Mass Disorient on you.
If none of the above works, make a couple of screenshots of what you're doing and post them in the Modding forum with a HELP! tag.
If the problem persists even without the mod, make a few more screenshots and post it in the Technical forum with an even bigger HELP!!! tag.
And, of course, have reinstalling the game in your mind as a last resort. Every technical support always tells you to reinstall your game first, whine later.