Theory 1 -- The only major variable you have tweaked is the lights, so my vote goes here.
Theory 2 -- I have experienced the exact same phenomen with my perpetual grow in 2014. I was around the 12th generation of Blueberry Gum from G13 Labs and my clones started to get smaller and scrawnier. Problem was I hadn't tweaked any of the variables on my commercial grow. Why mess with a good thing, eh? So, I'd suggest trying some plants from seedlings and grow them alongside some of your clones. See for yourself if the clones thrive as well as the seedlings.
Finally, I discovered that a good flush 2 weeks before harvest seems to up the bud size a bit.
Good luck, BigSteve.