On the services tab, what is the "Hide" drop down set to? If you have it set to "Parent Disabled" (the default) then set it to "None" and see if your missing service appears. If so, then this is most probably explained by the fact that the missing service does not transmit all of the time and when the mux was scanned it was not transmitting so TVH couldn't verify the stream and therefore disabled it.
The "Parent Disabled" functionality does cause some confusion (and frustration) from time to time. Search for the phrase on the forums if you want to know more.