Firstly
If you have finished the JAR IR, then the 25 hour JAR CPL SE course is reduced to 15 hour (as the 10 hour IFR section of the course is no longer required).
I think what you are asking is do the JAR SE IR at aerofan training hours count as PIC, the answer to this is no. If you have SE IR on your JAR PPL, and you then build hours IFR, of course this counts as PIC. THe only thing on your IR course that counts as PIC is your successful IR skill test.
HB