Something I've noticed, when switching between retail and FSO builds (3.6.5 and 3.6.9, specifically) is that beams have lost all of their kinetic punch in FSO. Because beams deal damage based on how long they remain on-target, this bug carries with it a lot of potential disruption of mission balance. I can set up a few retail-compatible test missions, if you like, but here's a brief summary of effects:
• Friendly AAA beam
In FSO, friendly AAA beam hits are pretty punishing, akin to being hit by a hostile AAA beam. In retail, you get knocked out of the beam's path, but don't often get more than one-percent hull integrity shaved off, regardless of what you are flying.
• Friendly anti-warship beam
As above, in retail, you get violently knocked about, but take very little damage. FSO often renders these as instant-kills or leaves you with such severe damage that you may be unable to feasibly continue the fight.
• Hostile AAA beam
On Medium and Easy difficulty levels in retail, hostile AAA beams scrape off three to ten percent of your hull integrity, depending on what you're flying and how direct the hit is (as glancing blows will toss you outside of the beam quicker). Moreover, they disrupt your aim, making it very difficult to lock on for a bombing run, while receiving beam fire. In FSO, on the same difficulty settings, the damage can be much more severe, particularly if you're traveling parallel to the beam, though your aim will not be disrupted at all.
• Hostile anti-warship beam
Any differences between retail and FSO are pretty hard to notice here, as most beams of this type tend to deal enough damage to instantly toast a fighter. Once in a blue moon, in retail, I've gotten lucky on a glancing LTerSlash or SGreen, but it's so infrequent as to be unnoticeable, when it stops happening.
Of course, the balance and damage issues are symptoms, as far as I can tell. The problem is that beams are supposed to knock you around, and at some point, they seemed to stop doing that.
A pair of caveats: I haven't investigated to see if this behavior persists in 3.6.10, but a cursory check of the documentation suggests the bug hasn't been noticed, nevermind fixed. Also, I signed up to Mantis to submit this, but after a year-and-a-half of waiting (on bated breath, no less!) for the confirmation e-mail, I think I've satisfied due patience well enough to post the bug report here.
In any case, though I don't say it often, you have made FS2 into a technical marvel for a new era and created a the definitive testament to what a dedicated community of fans can do. I wish you luck squashing this bug and any others that cross your path.