It breaks down like this:
6149 is used as the first season Desilu production number
5149 is the second season Desilu number
603 is the second season Paramount number
60043 is the third season Paramount number
My guess is they assigned production numbers per season and the pilots fell into one of two production groupings later used for production episodes. Without knowing what production tracking systems Desilu used all we can do is conjecture.