My weapons all have a very slight damage increase with the Omega Force armor worn, but none are +5%. My borg tactical prosthetic goes from 41 damage per bolt to 42 damage per bolt. My phaser pulsewave goes from 136 to 140 damage. All other weapons have similar small increases.
On a related note, every weapon I mouse over now shows that slightly increased damage, including ones I gave my boffs. So now I don't know what damage those weapons actually do in their hands, unless they share my bonuses
As I type this, I'm wondering if my passive bonuses from accolades etc. are affecting this. I only have like +10% damage from passives so it shouldn't be enough to affect the calculation this much (IE that +5% bonus is added to the weapons' base damage, which still does not explain the low actual bonus). The weapons' bonuses also should not affect this, as that pulsewave is [CrtH] [KB3] which does not add to DPS directly like [DMG] would.
Skills affect this too - all your percentage increases are additive from your base damage. Your Weapon Proficiency skill will also throw these things off and if you're tactical you also have Combat Specialist.
If I'm remembering how those skills translate into damage right, I'm guessing you're not tac, but have weapon proficiency maxed out. You're getting very roughly half the increase you would expect, which is consistent with doubling your base damage from skills.
Alternately you are tac and have both maxed... I don't remember if they're a straight percentage or cut in half.