I've been fighting a Service Charge System Message for awhile now. It all started with headlight flickering. Battery and alternator was tested alternator checked out but battery was showing weakness. So replaced the battery's then started getting the service charge system message. Replaced the alternator to no avail. Checked my connections and all is good. Now it's only intermittent at idle then goes away after driving. Sometimes it won't appear at all. With the scan tool I get a P0622 (Generator Field F Circuit Malfunction) code stored.

 

Check your grounds. There are several grounds to frame under the truck also and multiple connection grounds. Remove and clean thoroughly. Especially the PCM grounds.
Do a search on grounds here as there are many posts that cleaning grounds fixed a lot of weird problems.
Was your alternator a reman. or new. Lots of remans are junk so don't discount that. Low alt. output at idle is a sign of worn brushes in it.