"This version of Xcode cannot be used with OS X Server"

Ran all the updates on the Mac mini for 10.10.3 and associated items.  That included Xcode 6.3 (from the App Store).  Started Server.app and it asked to choose a new version of Xcode.  Did so and it gives the error in the heading.
Never seen this happen before.  Stuffs up any chance of using testing bots.  Any ideas on how to fix it?

I found it started working if I left it alone for a while.  After being contacted by an Apple engineer on Twitter it seems that after everything is updated it takes a while for it to run all of the initialisations.  So the approach seems to be:
1) Update OS X, Server.app and Xcode
2) Reboot, start up Server.app and leave it alone until Spotlight has stopped grinding away
3) Start up Xcode and give it a few minutes while it runs all the new initialisation processing
4) Select the Xcode item in Server.app and attach the new version of Xcode
It does seem to get there eventually but isn't helped by the worryingly incorrect error message.

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