Why does WLP002 sometimes attenuate more?

My 2nd most popular beer uses 002, we have this issue too. It just flocculates like no other yeast. We bought a stopper with no holes. On Days 2, 4, and 6 of primary we pick up the carboy and shake it into a fury.. ~5 minutes of real agitation. We do 14 days of primary so it's always clear by transfer to secondary time.

It does the trick for us, although I want try the krauzening technique Codehopper mentions.

I also thought about making a custom stir plate we could set a carboy in just for our one beer. It wouldn't aerate but it would stop settling. We tried other yeasts but nothing brings out the flavors we're looking for like 002.

It can be for a few reasons: 1. Underpitching (not enough yeast), 2. Insufficient wort aeration before pitching, 3. Cold shock, 4. Old yeast that you bought in a store -- well the last one is actually underpitching again. What to do: 1. Make a good 1.5-2 l starter, start it 2-4 days before the brew day, 2. Aerate wort well, not just swirl it in a fermenter for 5 sec, 3. Some say, slightly rocking the fermenter helps to rouse dormnant yeast (never helped me). 4. Krauzening. The latter made miracles for me. The idea is to preserve 1-2 liters of wort (put in a sterile bottle and in a fridge) at brew day, then ignite it with new yeast when your main fermentation is 90% through. When that small portion seems to be on fermentation peak, pour it into the main beer (I tried also "injecting" it into the yeast cake using a (sterile) pipe and a funnel, can't say it makes difference though). You can certainly do 1,2,4 altogether.