I don't know the details, but it seems they took advantage of eBay's ignorance. Screwing people over is not a good longterm strategy. I know I wouldn't want anything to do with them.
"EBay did not purchase this part of the Skype technology in 2005 because the Skype founders, and Joltid’s other shareholders, were asking for additional hundreds of millions, and stated that they intended to use the technology for other unrelated ventures, like their video startup Joost."
When one does a $2.6 billion deal, there is no ignorance regarding what is being sold. There are teams of lawyers on both sides of the table checking and re-checking every detail.
Likewise with Ebay.