There has been no change in Invoices that would cause this.

The setting in Receivables affects whether Retainage is calculated on the Invoice amount with tax or without it. It does not determine whether GST will be calculated.

Are you using a different tax group or just a different tax status to invoice the holdback?

If the GL Transactions show the full amount going to the Retainage control account, I suggest that you have a look at the tax group to see which account has been set on the tax jurisdiction.