QB Issue Resolution:

a reconcile just verifies that the checks that have been presented to the bank and those in QB match

any checks and deposits not on the statement will of course change the current balance

Resolution for Issue 'Even after reconcile process though quickbooks says the difference is zero for a bank account, it still shows a difference between Bank Balance & In quickbooks?' available: Yes (Solved).
Source: Intuit Community forum.

Even after reconcile process though quickbooks says the difference is zero for a bank account, it still shows a difference between Bank Balance & In quickbooks?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Banking
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Error Recovery for Banking [Canada]
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