I find there is normally a bit of difference from what my thermo reads and the air temp of the oven. Any where between 6 and 22 degrees.
I do put the thermo in the vac bag, taped to the mould.  I use the exposed junction thermocouples. I wouldn't worry about it to much.
(Apologies if I've got the wrong end of the stick).

That seems quite a high discrepancy, but did you allow some time for the oven temperature to even out? If the built-in probe is at the top of the oven, for instance, then the part temperature can take some time to read the same if it's sitting lower down. 

It's sometimes worth using a portable probe as a matter of course that has a couple of long string-like probes that you can stick to the part and use this device to reliably assess part temperature, especially in the early stages of a heating cycle

My oven was 20c higher than the setting on the pid controller when tested with a stand alone k type probe ' which is the best k type probes to use on these ovens please