I've since found a couple of conversations on the Google forums about this issue. It seems I am not the only one losing links to the new system and there is no fix in sight. My site which has the fewest links and I was building up, I have manually checked the existence of my inbound links and they definitely do not have the nofollow tag.
I thought I would try the old link:webaddress to see the difference and Google again reports no links to the site, although Yahoo gives me pages of them?
Interestingly enough though, there must be some inbound links of a reasonable quality as the Page Ranking has risen from 1 to 2!!
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