I'm not sure as IANAL (we've got our OGL/IP gurus looking further into this), I only know that:
1.) Publishers may get upset that PCGen datasets are getting converted to another program, we had to get a host of specific permissions to allow PCGen to create certain datasets. I'm pretty sure that any other other 3rd party who has similar software (or yes even one who supplies a converter to that software) would need the same permissions to create 'datasets'.
So I guess technically PCGen doesn't need to get involved here, it's a matter between the 3rd party and the individual Publishers. But we feel that we should at least inform 3rd parties of the permission gathering that we had to go through with Publishers. Who knows we might even be able to assist in helping other 3rd parties get those permssions (we've got the contacts after all ;p)!
2.) We _think_ (and we're investigating this) that the datasets the PCGen team have created are PCGen's IP. Now _if_ it is our IP then the team needs to decide who we allow to convert the data, I don't really see us blocking anyone but you are talking about a team of ~50 over 5-6 years producing hordes of data, so you can understand that there might be some grumblings about a rival software product benefiting off the back of their hard labour.
Now as the Chair Monkey I have asked the OGL/PI team to look into points 1 and 2 and I've also polled our entire team about point 2, the debate is raging at the moment

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PCGen has always had a history of trying to help other 3rd parties, so I think the team will end up voting to assist 3rd parties with point 1 (for the sake of relations between publishers and the software industry) and will simply only ask that we get mundo kudos for point 2

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I'll post up the results of our findings on this board and the digital D&D board on WoTC