The two links limit has been in place for quite a while - even before we moved to the new software - however it wasn't retro-active. If you haven't edited your signature for a while, then you wouldn't have noticed.
The limit is there to stop people generating signatures that overshadow the content and to limit CC's exposure to members who sign-up just to link-seed.
If you've got more than two links, just edit your signature now and again to rotate them.
Alternatively, put the links on a web page and link to that page from your siganture.
Cheers,
Shaun