My Mac Mini is new. I'm not sure if this issue was already there before installing Server.app. Unsusual things happen with the system on EVERY RESTART: Messages Agent ask permission to use keychain to which I say "always allow" and it pops up again till I say only "allow"; Dock gets resete (all customization lost); it always notifies me that I can download iwork for free but I already did; it always asks for icloud password. It´s like it resets some stuff every startup.
If Setup Assistant is running then the boot process almost certainly found no copy of /var/db/.AppleSetupDone
sudo touch /var/db/.AppleSetupDone in Terminal then reboot.
If you are having trouble after that with strange parts of the install process staying around then you may have some widespread permission problems. Use
Disk Utility to verify and then fix permissions on the volume and see how much that will fix after another reboot. You may find the problems still there on the first reboot after fixing them - it's the second that will tell.
I doubt if the Server app is causing anything as it really is just an application that provides a GUI for setting up some stuff already on your Mac.
I recently had this issue after having installed Mavericks, then used migration assistant to transfer my data from a HDD to an SSD. I followed every guide I could find, and none of the fixes worked for me.
Eventually I found a file in ~/Library/Preferences named com.apple.SetupAssistant.plist. In this file, I changed ShowKeychainSyncBuddyAtLogin to NO, RunNonInteractive and DidSeeCloudSetup to YES. This stopped the setup assistant from running for me, but now my dock won't save the fact that I don't want iBooks or Maps. I believe it is because of the RunNonInteractive flag, but am uncertain (and can't currently verify, as I'm making an image of my old HDD).