I highly doubt he had it back in 2006. That meant he had mono all of 2007...
Federer says "Apparently I already had it back in 2006, hints
There is no need to spin this as "Fed had mono at 2007", of course he didn't, in fact I think he was fit in general, but through the end of the year he did start to look sluggish phsycially and this is probably the explanation for it.
So uhm, no, this doesn't mean anything like "So that's why Roger lost FO!" or "Wow how did he win those slams, he's greater than we thought!"... In my very humble opinion, this is just another indication of the man's talent to control himself.