Users have setup several projects with default allocations, and have been submitting time against tasks where the ETC has been zeroed out. It seems that the ETC's are automatically populated. What would be populating the ETC's?
The population of the ETC upon assigning a resource to a task is going to be dependent on the resource's allocation % on the project which is why sometimes she is seeing zero % and other times seeing a value other than zero.
If the ETCs are required to be zero then you can zero them out and it will remove once Post Timesheets job is ran.