The Reconcile button should light up when everything matches up just right. We've seen before, though, where a fraction of a penny value was either imported in or inadvertently tacked on to a split Entry's amount, thus throwing off the Reconcile. So, it may be necessary to go back through your Entries, double-click each one, and get that value truly rounded up at the one-hundredth decimal place by double-clicking the Amount for each Entry. Once the value is set, the Reconcile should go through.
If that doesn't do the trick or seems like too much of a hassle, we could certainly take a look at the raw data in order to locate the discrepancy for you. So, if you're willing to send a data file our way, choose 'Backup Accounts...' from the File menu and attach the resulting file to an email to
support@splasm.com.