SOLVED!
Turns out that the problem was with an older JAMF script, secureBonjour.sh that we were using as part of a security policy for a subset of our computers.
The old secureBonjour.sh script had a separate routine to allow for machines running 10.5 and before, that actually moved mDNSResponder to /Library/Application Support/JAMF/DisabledLaunchDaemons/.
It determined which routine to apply by using an $OS variable, which was set by the output of the command:
/usr/bin/defaults read /System/Library/CoreServices/SystemVersion ProductVersion | awk '{print substr($1,1,4)}'
The awk statement is the problem here, as it returns only 4 characters: itβs fine through 10.9, but when we get to 10.10 it returns only β10.1β, which triggers the pre-10.6 routine and removes the com.apple.mDNSResponder.plist file.
This would have been a problem as soon as we rolled out Yosemite, EXCEPT that Apple had already removed mDNSResponder β so the routine did nothing, UNTIL they put it back. :)
So the fix for us was to remove the $OS check and the pre-10.6 routine completely (which is fine, because we don't support anything pre-10.7 at this point).
Note that it is possible to edit the awk statement to
awk '{print substr($1,1,5)}'
which would return "10.10" - however, I can't say what that would return on pre-10.10 machines so that may not be a total fix either.