Freeware is not the same as open source. Programs like WordPress are open source and free to use, period. Freeware often is free to use only for a certain period of time or so many uses. I do not know of any software to check it out, but you could consider this in re-evaluating your site for any problems. But that would not make them pirated unless they had been modified to strip out any limiting code.
Did you get the programs you offer from the download site of the program owners? It could be that the difficulty comes from data added by a site you downloaded from that identifies that site as the origin of the program when Google knows it is not. That could make the programs a security risk that Google would not want to be associated with.
An interesting question.