Warning: The Grants Module posts to the G/L Account Key. This entry may cause the account not to balance with the module

That is a warning because the journals are using AP as the journal key or because the journal account key is only supposed to be used from AP. This will depend on what GL accounts are being used. Typically foundations have a different account key for refunds, since it's not an expense.

There is a setting that controls that warning in system options. This option is set so that users do not use wrong accounts when doing journal entries, for example using an AP expense GL account listed for a refund when it should be a Refund GL account.