James Swan has helpfully explained where the missing blog comments have gone (link to his explanation). The bad news is - there is no way to turn off the feature that is causing these comments to disappear, at this time. The good news is that out of about 12,000 published comments, there appear to be only about 24 that have been "disappeared" by blogger's anti-spam software (on this blog at least) so far.
If your comment disappears, please let me know, and I'll try to rescue it from the spam folder. If you simply try reposting it, the spam filter will probably think that it was right, and you're just spamming ("Hey, that's the 15th identical comment: DELETE!").
There's another "known issue" that has been affecting Blogger blogs, including this one. Sometimes, when you try to publish your comment, you may get a "URI too big" warning. That does not mean your comment didn't publish. It just means that the URI that blogger has generated to get you back to the blog is too long for either your browser or some other piece of the Internet architecture. Don't worry about it. The comment probably did publish. Go back to the page you were on and check (use the browser "back" to get there).