Welcome to our forum.
Chad, do you use dichlor in your spa? The N2 beads will fuse together over time as they breakdown, especially with the use of dichlor. Mine only did it on the top as well, I'm assuming more water flows through that area. I flipped mine over, because I'm a few weeks shy of the 4 month mark. I checked with my dealer and they said this is normal. I don't have any spots in my tub.
If it's black algae, it's not uncommon or unusual that it came back. Black algae does have to be scraped off. Can you smear it if you try? It's very resistant to treatment. You could try lowering your ph to the 7.0 to 7.2 range, then get a chlorine tablet and try to scrape or rub off the spots with that. Black algae has a covering that makes it hard to penetrate with chemicals added to the water. Each spot needs to be scraped. Then shock. The pictures definately look like they are "growths" attached to the spa and growing out from it. Black algae is usually larger than your picture, unless it's just starting. Yes, the beads are supposed to get smaller. They are designed to dissolve slowly into the water. When adding dichlor or shocking with it, they can dissolve faster. When they are soft and mushy they clump together.
I'm calling in a pool and spa water chemistry expert to check it out in person. I'll pay whatever they want.
I used N2 for the first year of my tub and then simply got tired of messing with it and went straight di-chlor and save the $100/year