Not a dumb question, and no - the S on your confirmation had nothing to do with it. You were selected because either the ID checker or the TSA person checking your ID called you for a secondary inspection as part of their asinine 'continuous screening' program. If they don't have enough branded 'victims', they can start pulling people for secondary search at random - or for any other reason the ID checker or nearby screener can conjure up.

On the other hand, it wouldn't surprise me if the braintrust checking your BP decided for themselves that the "S5" on the BP really looked like an "SS", and even being in the wrong spot of the BP, they decided it meant the same as "SSSS" or *S*.

You have nothing to lose by telling the ID checker "no" - the worst that can happen is you get it anyway. At a busy airport with multiple checkpoints, you can tell them to bugger off, go back to the EService machine to print out a clean BP and go through a different checkpoint, but you need to balance the cost in time vs. just letting them do their little play thing with you and being done with it.