As long as the hours are legal and are gained in a manner that would be acceptable in accordance with JAR-FCL then it does not matter what licence you used.
An example of hours that would not count is the common US system of two pilots flying together and both logging PIC time. Most common with pilots who hire twins at very low rates for hour building - the rate being so low because there are two pilots logging the time!!!!!
So as long as you were legally and properly licensed as PIC and the only PIC on that flight then there would be no problem.