I would say its the wood if the water is just turning an off color, the best thing to do is get some high-grade carbon for your filter. Some filters have optional carbon inserts otherwise you can buy it buy the box and put some in with the other filter material in your filter.
The carbon does need to be change every couple of months to prevent the build up of toxins going back into the tank.
As for the chasing the males were probably just finding there place in the pecking order, you really need to have a 3:1 ratio females to males, this spreads out the males desires between all the females.
Hope this helps.