Yep that PH is locking out nutrient absorption. What were the flush numbers, it generally takes using 3 times the vessel size for a flush 
I just did a gallon in each 3 gallon pot and runoff barely raised to 5.1. Im going to mend in some fine dolomite lime in a few days and just water with 7.0. I didnt want to start making drastic changes all at once.
@WhoDey as @OGIncognito stated, it takes 3 times the pot size to flush, so your 3 gallon pots should get 9 gallons of water to flush, not 1 each! Another 8 gallons might see that pH rise to the upper 6 range.
And don’t be afraid to make drastic changes, some plants need it
It took me 3 times to flush with 3x water because I didnt use dolomite in soil mixing.
Now most my watering is 6.6-6.9, going in.