Here's my observation: On 3/26 I flew from IYK-LAX and LAX-CLD. 24 hours prior I printed out both boarding passes at home with seat 9C selected. When they tried to scan my boarding pass at the gate the barcode wouldn't read -- not even that it was rejected, but wouldn't even read. The gate agent printed out two new passes for the flights with me in 6C and 11D. 9C was taken on both flights. For the return I picked both seats in 9C again, and at the airport my boarding passes printed with 6C and 11D again. Something is definitely awry. Fortunately on the return 9C was open.

I have the same concern as the OP, though, with upcoming travel with family on separate itineraries!