Agreed, same thing happened with me using Mozilla Firefox with Private Bookmarks, one Tag per Bookmark.

About a month ago, there seemed to be a one or two day delay before a Bookmark would show up under its proper Tag. Your Bookmark exists, and can be Exported, but currently it seems that they take a long time (or never) to show up under the correct Tag.

Perhaps this is due to a huge delay in Reindexing, as Joel Liu mentions?
http://groups.diigo.com/Diigo_HQ/forum/topic/how-long-will-it-take-to-make-diigo-work-again-rant-44763

Try the following...

EDIT A BOOKMARK'S TAG AND SAVE IT
Pick one of the problem Bookmarks in question,
Edit it,
change the Tag to a Tag that doesn't exist,
Save the Bookmark with the new Tag.

EDIT THE BOOKMARK'S TAG BACK TO THE ORIGINAL
Click Bookmarks,
Edit it again,
and change the Tag back to the Tag you actually need,
Save.

WAIT
The number of Bookmarks under the Tag you actually need will be up-to-date,
and the actual Bookmark will be under the Tag in one to two days (!).

THANK YOU
Until Diigo develops an enhancement to rectify this,
we'll need to do these updates manually.
*sigh*

Let's keep sharing Diigo ideas!
Frank Seto
http://ifranks.blogspot.com

Joel Liu,

One solution might be to adopt the system that is in-place for web applications like Blogger.
Email addresses could be used so that users could Email a Bookmark to their own Diigo account.
This would mitigate any sort of browser incompatibility issues, and truly allow users to add Bookmarks on-the-fly.

Example:
TO: franks.PersonalPostingCode@diigo.com
SUBJECT: Tag(s) entered here
BODY: URLs of the site(s) in question entered here