I'd bet the SEO is the problem... the link being submitted to twitter is the non SEO link, but when you visit the thread you are visiting from a different URL so the counter is zero and always will be.
I noticed the same issue if you tweet a post immediately after you submit it... when you submit a post the URL has the post number appended to the end of the URL, when you browse the thread from a forum though there is no post number just thread id so it's a different URL so the counter is different.
The way around this I believe would be to use a canonical link tag in the header but that would be very bad for your SEO purposes because you want the 'seo optimized' url not the vb default one.
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