How did you enter the cheque as it sounds as if you included the vat at the time of cheque entry. The credit amount must equal the full cheque amount.?
Resolution for 'cheque entry issue: 'VAT not showing in set credits' available: Yes.
The cheque entry 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 cheque entry issue yourself by looking for a resolution described in the article. If it is a complex cheque entry issue or you are unable to solve the issue, you may contact us by clicking here or by using other cheque entry support options.
For more information about resolving issues related to cheque entry in Quickbooks/QBO or to get support for the issue 'VAT not showing in set credits', click the link below: