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Glad to know it works, even if I didn't have anything to do with that!
Did you set up timing constraints for the RGMII I/O pins? If putting a ddio for the clock line it could indicate a timing issue. I didn't think it would matter for a 25MHz clock, but maybe it does after all.
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I did not setup any constraints on the RGMII pins specifically, I assumed that the TSE files had something in there for them. Perhaps that was a bad assumption.
I got the idea of the GTX clock DDIO from the DE2-115 Dev Kit Web Server Example. They do the same exact thing there, shifting the output clock by (~1.5ns).
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