After reviewing the end user install, I see that Splunk DB Connect 1 ver 1.2.2 or lower is installed on the Splunk Instance with the issue. As the app is not rated for Splunk 6.4 according to Splunkbase it should not be on the system, but it is.
Way to fix, is you have to remove the entire app from the Splunk File Structure, restart splunk and you should be able to see the remote inputs again.
Disabling the app will not correct the issue, you will need to remove the entire contents of:
%SPLUNK_HOME/etc/apps/dbx
from the splunk system and restart splunk service for the changes to take affect.
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