I don't know what you've done to the pirates but they are really viscious now.
I got a bit of shock in my first pirate battle, a 5th Rate Frigate 40 guns v a Pirate sloop and a brig. I thought it would be a doddle as usual but these guys were on steriods or something. The sloop just came straight at me and boarded, damn near killed a 3rd of my crew, and blow me if as soon as I cleared them off the deck the brig charged in and boarded as well.
Managed to win but I only had about 60 crew left.
Same with the Barbary pirates, I boarded one of their ships with a 2:1 advantage in crew strength, and they were 'Shaken' from close range grape prior to boarding and I still lost.
Mind you the Fluyts look like they've been nerfed in some way. I've come across a couple of them so far and they seem really slow now. My 5th rate was literally running rings round them.