Depends on how the charger worked. If it actually metered the current it was putting into the battery it would stop after it let 6000mah worth of current through the battery and think that the pack was full, but the pack now being 8400mah it'd never get full. Also if it was doing a fixed charge rate and looking for a voltage dip as the pack was full the higher capacity pack may cause the voltage change to be slight enough that it can't properly detect the charge state of the pack anymore. Depends too much on the exact method the charger used to detect battery state and manage it.
Where'd you get the new cells from? Some battery surplus suppliers will sell you brand spanking new batteries that are actually old stock, and weather or not they're used Lithium Ion batteries will go bad on the shelf. I'd be a little cautious.