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If I search for "www.mydomain.com" (with quotes) all of the sites that have links to mine show up. If I search link:www.mydomain.com I only get 2 of them. None of these are javascript links and some of them are my internal links.
I only have three sites that I have recip. links with. So I doubt that it's a recip. link penalty. What I suspect is that somehow these sites have not been crawled in a while and to keep the backlink count fresh Google may have some sort of exparation on backlinks. (just my theory) That would explain why they show up in a search for the domain, but not for the backlink search.
If I had to guess it seems like Google is playing with the backlinks probably as some sort of upgrade. This being the case I would bet that number of backlinks doesn't have much weight right now, then again, if everyone is loosing the same percentage, then it is probably best to have as many as possible.
My SERPs are not scaring me right now and I know my incomming links are still strong so I'm not going to worry just yet.