Yeah different rocks will mess with water chemistry. If in doubt scratch off small pieces of the rock into some water, mix it up, and then do before and after tests for PH and hardness(GH). Off the top of my head I know rainbow rock and limestone are also bad for Bettas. They will raise the PH too high.
Have you tried frozen peas for its swim bladder issue?
http://www.ehow.com/facts_5608361_betta-swim-bladder-disease-treatment.html
You can also try fasting him for a few days or even longer. It takes a long time to starve a fish to death.
If he is building a bubble nest he can't be doing too bad, they don't do that when they are stressed. If he is struggling a bit to move around I would buy a fake silk plant, then place one or two of the leaves about an inch under the surface so it can rest on it and be close to the surface. Much better than resting on the bottom.
The start of Betta care depends on if it's in a cycled tank with a filter, or a non cycled tank with no filter. Both require difference maintenance, specifically how water changes are done and their frequency.