After hearing that, I would say is sounds like a internal generated CT.
Check all of your courtesy tone assignments.
Like these that were default for v1.01
ct1 = |t(350,0,100,2048)(500,0,100,2048)(660,0,100,2048)
ct2 = |t(660,880,150,2048)
ct3 = |t(440,0,150,4096)
ct4 = |t(550,0,150,2048)
ct5 = |t(660,0,150,2048)
ct6 = |t(880,0,150,2048)
ct7 = |t(660,440,150,2048)
ct8 = |t(700,1100,150,2048)
If that confuses you any and you just want to quick test something
try changing which is selected with one of these. (set default with v1.01)
unlinkedct = ct2 ; Send a this courtesy tone when the user unkeys if the node is not connected to any other nodes. (optional, default is none)
remotect = ct3 ; remote linked courtesy tone (indicates a remote is in the list of links)
linkunkeyct = ct8 ; sent when a transmission received over the link unkeys
;nolocallinkct = 0
Remember which one you changed when it went away and check the description for that CT.
If it is happening conditionally, you need to figure out what are the conditions when it is present to figure it out any more.
i.e. what node or device input.
But yea, you still need to listen on the input to rule that out.
Specifically if it is on the output of a rf link.
edit:
There can be many reasons for this depending on where it is being generated.
But one other thing is perhaps a tone macro set to play a CT ?
Scan your file and be sure it has not been set for something like that.
Also some nodes who are linked and not configured correctly that output their CT before drop. True when you have a strange config of duplex mode and perhaps linktolink set.
You can also query last node to transmit or watch the asterisk verbose output when you are listening to your net.
Just some thoughts in leads to check.