I lean towards believing the PH pen more, but then I cannot get my head around how the drop checker, which is supposed to be isolated from external influences, does not tally up?
Provided you haven't contaminated the drop checker fluid it will be right and pH pen wrong. The absolute value of pH is being affected something else in the water. You are all heading down the Matrix of misleading numbers game. Hey my latest gadget reads 6.8 (or what ever) so something must be wrong, what must I do.....
If your water is soft the pH pen will be hopelessly wrong, I think you need at least 4KH before you should even consider a reading. Oh you don't know your KH so how can you trust your pH reading.....If you claim you know you KH from where ?? Most hobby test kits are really alkalinity test kits oh which rely on pH to read KH....see the circular Matrix of numbers.....
Your drop checker is indicating there is still residual CO2 in the water, fine no problem with that, you have gone to great effort getting CO2 in there, not a problem. My drop checker often stay green next morning depending on spray bar angle, air pump not being on, age of drop checker fluid etc etc. No problem. I take the drop checker out and within 1/2 an hour it is dark blue.
The only thing you can rely on with the pH pen is the rough differential change in pH of 1 unit drop. Some people need 1.5 pH drop or greater to get their drop checkers green. In a tank you cannot correlate the KH value with absolute value of pH as there is so much else going on in the tank. Luckily these things cause you to under read pH values (acidic) thus you get a 1 pH drop with only 20ppm CO2, so you under dose CO2 rather than overdose and kill your fish.
So in summary, aim for 1 pH drop due to CO2 at lights on as a good start, you will probably be under 30ppm CO2, so safe start there. Use this in conjunction with drop checker, plant health and fish activity to gauge CO2 levels. Don't rely on the numbers too much, use the numbers in conjunction with what you see and work on that.