Fascinating. I'm sure this is a bug.

If you look in, say, Rose::DB you'll see that they use 2 different kinds of links. The first is for ones in the uploaded distribution. The second is for ones which are in some other distribution. In that distribution it gets them right. The problem is that you are getting the "not my distribution" type of link for Inline::C-Cookbook, and it isn't working. Your good links are of the direct kind. I don't see an option for having 2 kinds of links in Pod::Html, so they are probably using some kind of custom parser (possibly derived from that one).

(Possibly related is that in perl 5.8 if I type in pod2html Inline.pod > foo.html I see 5 warnings about being unable to resolve links. It is unable to resolve Inline-Support (2x), Inline-API (2x) and Inline-FAQ (1x). It does think it can resolve Inline::C-Cookbook. The difference is in the function page_sect in Pod::Html. It has conditional logic with a branch for /::/ that has different logic than the final else. If they hacked up that to get theirs, then this might be related. Or could just be coincidence.)

So at this point I am confident that this is a bug. http://search.cpan.org/feedback has advice for how to give feedback. I'd use that to report the bug. In the meantime my original suggestion for renaming the file probably will succeed in working around their bug.