The only ph pen I use is the Hanna 9044 which you will not find in stores. Call Hanna for a local distributor and you can get it for 119.95usd. It does constant monitoring of ph microsiemens ppm and temp. For pens it is best to keep the diode constantly wet. If it drys let it soak in water for 30 min. for an acc. reading. If you still have a prob with the spots you may want to flush the 3 gallon pots out with like 9 gallons of water. Your plants may be drupy from a low lumen that is given by flouros. Most of the time it is from the bottom of the pots never drying out though. The three gallon would be best if watered with a garden sprayer to keep the bottom mostly dry as they will take a long time to dry out. A good water source you may want to consider is from a dehumidifier if you only got a couple plants. The clorine in tap water will disapate in 24 hours if you let it sit. I use two gallon max for indoor mothers at 2 feet tall so the roots can get oxygen. The spots can be from a unbalanced ph in the bottom of the soil. Microorganisms as they convert organic nitrogen into inorganic form which the plants can use raise the ph up. If the bottom of the soil is left constently wet which can be an issue with 3 gallon pots if not using a sprayer will not have oxygen for micro life and the ph is not the same as the rest of the soil which can cause burning. The transplant my have allowed the bottom roots to dry. The rooting powder has auxins in it but shultz is inorganic and thrive alive has the same hormones in a organic form derived from norwiegin kelp. I only use 1 to 2 drops per gallon as well even though they reccomend 15ml per gallon, but that is for sales only. Since I have never seen batguano burn I would lean towards a ph problem at the bottoms of the pots from not drying enough.
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