I played through Inferno R1 lask weekend (using a very new nightly build with Inferno SCP patch 2). I can conclude that some missions were broken for me too. Olemus missing 100% of its beams, Hathor firing only 1 salvo, Gigas not firing at all, etc...
So wait a minute!
All these issues are beam related issues!
I had flashback about the first SOC mission in the FS2 retail campaign. Somewhere down the line a FSO patch broke that mission, meaning that Iceni can no longer destroy the Sobek at all because it only fires 1 salvo of beam fire. If player doesn't take out the Sobek's main beam turrets in time, Iceni is doomed. The mission is now considerably harder than it was in FS2 retail, where Iceni destroys Sobek in a very short time. AFAIK the final version of MediaVPs_2014 hasn't fixed this mission in a reliable manner. The Iceni still gets passive 4 times out of 5 (I did some considerable amount of repeated tests with that mission yesterday).
Would it be wrong to say, that Inferno has suffered from this same issue as the first SOC mission has?
I'm a noob fredder myself, so I only know about the basic functionality of Beam-Free SEXP. Can any advanced fredder answer me, what are all the other methods of making capital ships fire their beams? Are some of those methods broken now? Would it be possible for SCP to revert to some older functionality and fix them?
For example, would it be possible to pinpoint to exact reason why the Hathor can't destroy those weapon systems of Gate Station anymore? Or what's up with the targeting of Olemus? Why does it miss?