The "idling" signal is constantly being modulated with a "no op" signal that keeps the locomotives alive. Maybe the scope just captured different segments of the FM signal, once with the lower frequency, and the other with the higher frequency.
With a conventional counter set to a relatively long sampling period, I read 454.88 kHz according to my notes.
The signal is generated by one of the digital chips and then shaped into the sinewave by some LC filters. Seems like the frequency should be quite accurate since the clock for the system is a 34.35 MHz crystal, but I guess the filtering could be off frequency enough to attenuate the signal.
My (incomplete) notes indicate that the digital version of the signal passes through a double LC filter (L1 & L2 in series, C's shunt to ground), then to the emitter follower TR5 that has a 100 ohm emitter resistor R3, and then through some L's and C's to the output pin (that aren't on the TMCC Base's output). Plenty of opportunities for a bad component.
Check the base of TR5, and I think there is also a test point after the first LC filter L? and C2 after the emitter follower. Moving on to the next PC card, C1 is the output coupling capacitor that was damaged on my Base. L12 and L17 carry this signal to the stud terminal.
Let us know what you find.