Potentially, they are doing this to try and prevent those with malware from using their service in an attempt to decrease fraud? It does raise some concerns though. Is what they are doing legal? I know that if I started port-scanning eBay, it definitely would not be considered legal, so why can they do it?
In the article written by The Register, it appears they are testing at least 13 different ports. This data then appears to be sent to ThreatMetrix, who are no doubt helping collate this information for eBay.