Testing for this issue included checking to see if there was a "Run InterProScan..." button (including ellipsis) and making sure the option was available under the ProtAnnot menu. I also made sure the button/option opened to the IPS Job Configuration window and that running of the IPS tool was not affected.
Since this issue is resolved it will now be closed.
The Run InterProScan button should contain ellipsis (...) to signify that there is more input required after clicking the button.