[coopduc]

In general, parts won't take dye because they did not anodize or the ano is very thin. Assuming you area calc is correct, it appears you applied the 720 rule correctly, so the next likely culprit is the electrical connection to the parts.
Were you actually able the draw the amperage per your calc? Make sure all the connections are tight, including hangers holding the parts. Hangers should be forced into some feature on the part, not just hung on a hook. Check the sticky on the importance of good connections.
Are hangers titanium or al? If al, it it new or if previously used in anodizing, freshly stripped? With the part racked as ready to go into the acid, check for electrical continuity from the anode to the part with an ohm meter. You should have no resistance.
You also don't say much about the parts themselves. Are they newly machined from 6061 or previously anodized parts that you are re-doing? If previously anodized, it seems to me that your lye solution may not be strong enough to strip the old layer off. For stripping, use 16 oz/5 gal. If you're using it as an etch for bare 6061, it may be ok but likely not necessary. I don't think it would solve your problem, though.
Similarly, 10 min in the desmut sounds excessive, 3 min should be more than enough for even the smuttiest 2xxx parts. 6061 typically smuts very little.