My development system shut down times increased from a typical range of 30-40 seconds to almost 3 minutes when I installed FMPro Server 14. The system has an Intel i7 Processor, 16Gig Ram, 1TB SSD, and OSX Mavericks, with multiple versions of FMPro, and one instance of FMPro Server 14.
Turns out this shut down delay is due to a setting in the FMPro Server preferences. I was able to get back to the original settings by doing the following:
1. Locate the Library/launchdaemons/com.filemaker.fms.plist file, and open it with a plist editor or text editor.
2. Change the "exittimeout" from 120 to 10 seconds and save the file.
3. Reboot. From this point on, your shutdown times should return to normal.
So far, I have not found any problems with this approach.