I recall having to add a patch, and it may have been to enable the switching of the external reference. I have never used my Rev D Pluto with my Portsdown, so you'd be on your own if you tried it, but I doubt it can do anything dreadful. I'll link to the patch on my server so you can grab it and try it if you like?
http://www.chriswilson.tv/patch.zip
Read the text file within the zip, it gives info on version compatibility. Personally I'd just patch your firmware and wing it ....
I am pretty sure it was needed to enable the external reference, now I cast my mind back, as I do not need or use the PTT stuff.The interrogation stuff looks as if the external clock *SHOULD* be enabled, so it must be something else. It's all a bit of a minefield mixing and matching firmware with various hardware at times.
Good luck.