I'm not sure I can directly help you, as I don't have a cell plan for my N900 currently, but to clarify...
- When you mention the number of new SMS messages, are you talking about in the Conversations app, the Notification (e.g. "Orange Bubble"), or something else (e.g. the Conversations desktop widget)?
- Which text is blue?
- Is the problem that one particular message is not getting marked as "read" once you read it, or that it shows one more unread message than actually appears in the list?
A screenshot might help show what you mean (the load-applet package adds a screenshot button to your status area, if you don't already have that installed).
Cheers