If you are monitoring a large trunked radio system with a lot of sites (i.e. Palmetto 800), you may want to read up on
affiliation as that may be a factor in your ability to monitor specific talkgroups. If a talkgroup is not used by many radios in an area, it may appear and disappear regularly from the sites in the area.
Something that I dislike about the current Whistler scanners is that it tries to think that it is smarter than the user, so simplifies multi-site operations to where it locks onto what it thinks is the best decoding site and sticks to that site until it determines that the decode is not good enough. What could be potentially happening is that when you first turn the scanner on, it locks onto a site that does carry the talkgroup you want to listen to, but then it switches to a different site that does not have your talkgroup. It could also be related to radios switching sites and are therefore no longer being affiliated to the site that the scanner was sitting on.
One thing you can try is to program the talkgroup into multiple systems each having only a single site that the talkgroup can be found into the same scanlist. This forces the scanner to routinely scan through each of these "systems" for that talkgroup instead of locking onto the first site it determines as having a good decode.