The link: command now only shows a small, bizzare subset of the actual links. There's a possibility that if you don't have a lot of incoming links, the subset shown is down to zero. At any rate, I wouldn't worry about it much. Google's link: is basically useless these days. Its main function is to confuse webmasters - it isn't representative of what G really uses in the algo.
All of that said, you could take a look at the source code for a few of your quality incoming links and make sure things are cool on that end, (i.e. straight-in, normal <a href=""></a> tags). If things look good, forget about the link: cmd
Better yet, check Yahoo for the Link command. google only reports about 1/10th of what Yahoo records. I've been watching Google link vs Yahoo link for over a year now and the amount of links that Google has been reporting has been steadily decreasing each month. But Yahoo doesn't record them all either.