It seems this problem has resurfaced again with the new version of Mac OS X. More specifically, this problem seems to affect appending search domains when the hostname contains a dot. In Yosemite (10.10), mDNSResponder has been replaced with discoveryd. Fortunately, all we need to do here is add the --AlwaysAppendSearchDomains argument to the LaunchDaemon startup file and everything should work as expected.

1. Before you do anything, make sure you have updated to at least OS X 10.10.1.

2. You will need to edit /System/Library/LaunchDaemons/com.apple.discoveryd.plist. Add <string>--AlwaysAppendSearchDomains</string> to the list of strings in the ProgramArguments <array>.

3. Restart discoveryd to see your changes take effect.

   sudo launchctl unload -w /System/Library/LaunchDaemons/com.apple.discoveryd.plist
   sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.discoveryd.plist
   

4. Profit!