Actually, it was affiliated with PPT if my memory serves me correctly. Illusen's Glade changed it's forum hosting as it was suggested by the owner of PPT (see above) that he could no longer host the forum. The affiliation that did exist, had long since rotted away by then, however.
It was affiliated through connection really. Janie was an Admin of the PPT Forum and the Owner of the Guild at the same time. If Yukio suggests that it was a 'good deed' he did on Janie's part, well I would suggest it was more a case of payment for services rendered for the creation, administration and upkeep of the previous forums. (no small feat in itself)
TNO is also separated from PPT now, in order for Yukio to continue with his advertising popups and banners. TNT do not allow advertising and neopets images on the same fansite pages that generate cash revenue (hence the reason for the lack of neopets images on ppt in general these days).
So in short, yes they were, but now they are not. It's an agreement that both parties have become entirely happy with as far as I can tell.