Mail has incorrect "index"

Mail on my iPhone shows an incorrect index and message count.
This is what I mean.
Message count. In a given folder (any folder) it shows the msg count to be several thousands. That may be true in the whole account but not in the folder. Also, each folder shows a different count in the thousands.
Like many I read mail on my iPhone and on my computer. Here's the idea.
During the day I check my e-mail on my iphone (latest firmware. NOT jail broken). I do what I can with it on my iPhone and then deal with the rest on my computer.
I then delete things from my computer and it's still there on my iPhone after refreshing.
I use IMAP.
Things work right between Thunderbird (latest), Mail, and my iPad (latest firmware. NOT jail broken).
Any ideas? Before I send something to Apple.

Bump.
I forgot to mention I am NOT using gmail.

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