QB Issue Resolution:

When you have the register open, at the bottom left corner, is the Sort by :Number/Ref. The deposits will be at the very top. The default Sort by is ” Date, Type, Number/ Ref. It’s a great feature to find spacifc things you are looking for but can be confusing.

Resolution for Issue 'Deposits not showing up on check register' available: Yes (Solved).
Source: Intuit Community forum.

Deposits not showing up on check register: 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 Deposit
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Error Recovery for Deposit [Canada]
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