The payroll.ini file is created the first time that you open Sage 50 Payroll, rather than when you install the software. Because the install process didn't create the file, the uninstall can't remove it.
NOTE: If you have a second installation on the computer, it's important that you don't remove this file. If you do remove it, this resets the configuration settings for the second installation. This might have a negative impact for the settings in the other installation.