I subscribe to the baka-updates manga rss feed in google reader and it looks like a lot of entries don't show up now in the feed there even though they do appear in the plain RSS feed. There's also a bunch of duplications sometimes.

Google says
"Items in my feed do not show up in Reader
If a feed reuses GUID tags, Reader will treat them as changes to the original item and not as distinct, new entries. You'll be able to find them by scrolling back in the feed to the original entry."

but I don't see GUIDs used in the BU RSS feed. Any ideas on how to make the RSS feed work properly in google reader?

Same here... a lot of entries are missing in Google Reader. Hope this can be fixed!

Not sure. Try increasing the rate of updates for now to 5 minutes or something.

As far as I know, there is no way to control the update frequency in Google Reader. (The update frequency is determined by the number of user subscribed to the feed) But I feel that the point mentioned by squeeqwer (reusing GUID) might be correct since I notice that series that updates frequently (such as Naruto/Bleach/etc) are the one that missed/not shown as new entries.