This is an issue where new / old versions of items are "Account bound on acquire" vs. "Account bound".
To fix this, put all the items that don't stack into your inventory. Then change maps or logout and log back it. After this, the items should stack.
It's annoying, and ANet is aware of the problem, but at least there is a workaround.
kalendrafMember Since 24 Mar 2011
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Henge of Denravi