Edited to add: I opened an LJ support request and got this response, and now it's fixed...if anyone else has had the same issue!:
This may be related to a new spam related option LiveJournal implemented a few weeks ago. When you visit the entries where these comments were posted, do you see a 'xx suspicious comments' link appearing with the other 'post a comment' style links? If so, click that link and see if the missing comments are there.
The "Spam Protection" checkbox [http://www.livejournal.com/manage/settings/?cat=privacy], when activated, will mark any comment containing a link to a non-whitelisted domain as being 'suspicious' -- they are screened and moved to that special section. You can mark them as 'not spam' to return them to being visible on the main comment page.