Correct way to control 12V relay from a Raspberry Pi
The problem with PNP circuit is that the Raspberry Pi works on 3.3V while your Vcc is 12V.
So, putting either a low signal (0V) or high signal (3.3V) always will turn on the PNP, because in both cases VBE = VCC - Vbase = about 0.7V.
The base current will be either (12V-0.7V-3.3V) / 1k&Omega; = 8 mA or (12V-0.7V-0V) / 1k&Omega;= 11.3mA.

Since you already have the printed circuitboards you should implement the NPN version.

EDIT
Regarding the NPN version: as you commented you need a NPN with the correct pinning (i.e. with collector and emitter swapped) like the MMBT9013 (don't know if it still exists).

Other solutions i can come up with require rework (don't if the number of PCB's and/or the space on the PCB allows for it)


putting a 9.1 zener in series with R10 using the pads of R10 (placing the components diagonal like /\ instead of --)
you may need to lower the value of R10
replacing the PNP with a PMOS (e.g. NTR4171P), solder an 1k 0805 resistor on top of the gate and source pin and replace R10 by a tiny 9V zener (no idea what package R10 has, but e.g CDZFH9.1B)