When using the same Pay Code with multiple rates of pay, TimeTrex will split these out into separate line items on the Pay Stub to be as clear as possible. However when running reports, it will not do this if you have any kind of group options selected on the report, as it would be impossible to do so while still performing the group operation (though, you could group by the Pay Code and Hourly Rate to mimic it). When using multiple rates of pay for a single pay code, the reports may not show the Hourly Rate that you expect, since TimeTrex does a "simple" average (not a weighted average) of the hourly rates when grouping or sub-totaling, similar to if you had a column with each hourly rate on a different row in Excel and asked Excel to calculate the average of the column. The total time and dollars would be exactly correct though.
Pay Stubs and Payroll Export reports (when exporting to a specific format) are handled differently since they can't be arbitrarily grouped, so in those cases TimeTrex will create a new line item for each different rate of pay, even if the pay code is the same.
In short, if you want to make sure the hourly rates are never averaged even when arbitrarily grouping them in reports, you will need to use a different Pay Code for every hourly rate, or always include the Hourly Rate columns in the group selection.