If a newly added pay code that has been usable throughout the system was not included in your upload file, it is probably just missing the Upload Code or the Upload Order values defined on the Pay Code Management screen which can be accessed through the Pay Code link under the PEP tab.
The Upload Order value tells the system how to place or group the codes in the export file. Pay Codes with a value of 0 are not included in the upload. Pay codes placed in the export file by their Upload Code and are grouped by the Upload Order value of 1 being first, 2 being the next group and so on.
If the entire pay code is missing from the file, make sure the Upload Order value is not 0. Records with an upload order of zero will be excluded from the upload.