The issue described is likely due to the order of execution in Salesforce, where processes in Process Builder run after all before triggers. If the Opportunity's Amount is changed and the CommissionBaseAmount__c is set by Process Builder, the trigger that calculates CommissionAmount__c may not see the updated value if it operates before the process.
Replacing the process with a before-save record-triggered flow (formerly known as Fast Field Update) would ensure that CommissionBaseAmount__c is updated before the trigger runs. In a before-save flow, field updates occur before any Apex before update triggers fire, which means the trigger would have the updated value of CommissionBaseAmount__c to use in its calculation.
eferences:
Order of Execution in Salesforce
Before-Save Record-Triggered Flows