Will running optimised BIONC core program affect results?

The BOINC Core Client version doesn't affect the results at all, they are solely done by the Applications.

The Client might have a minor impact on the crunching time (depending on how much CPU time it takes for itself and the priority setting it starts the App with), and of course on the benchmark results, thus on the credit claimed. A buggy client may cause more "client errors", but that's about it.

BM