I am not sure what is going on here. I just ran both these queries, and tags worked for me. I looked at the html/css of the flash and image pages, and it seems to be the same. I would say that perhaps e621 was busy and giving sporadic 503 errors or something, and those were being silenced by the tag parser for some reason, but if the page with the tags doesn't load, the parser shouldn't be able to get the image url either, so it should all break.
Is it possible that your new files are getting tags, but existing files aren't? Hydrus remembers what urls it got its files from, if any, and doesn't bother to download again if it knows it already has/deleted the file. In some cases (usually subscriptions atm), the client also won't bother to re-download tags for files it already has downloaded from somewhere.
BTW: Although the 'littlenapoleon' tag has a count of 34 on e621, the gallery page actually has 38 thumbnails–I guess they don't count some dupe files or something? Are the gold/green borders something to do with that?