3-Phase Permanent Magnet Alternator with Regulator/Rectifier (SCR) Output Waveform
The first part with the windings and the diodes of the three-phase alternator turn sine waves into dc.  

Each of the three windings produces a sine wave phase shifted by 120° (red, blue and green).  The diodes eliminate the negative half of the waveforms (dashed lines) creating humpy dc.  As the crest of one waveform drops, another peaks so the ac waveforms have been converted into a  dc waveform (black).


This is the waveform you are seeing at the start of screen capture.  This should be around 13.5V for a 12V battery.  This depends upon your battery voltage.

The second portion of the circuit with the SCRs and the regulator is designed to turn on if the output of the first section is above 13.5V.  It is designed to prevent high voltages on the battery by bleeding excess current.

This is the waveform you are probably seeing at the end of screen capture.

You have your scope in ac mode so it is difficult to tell the true voltage levels.  Similarly, it is difficult to debug something without hands on, but I'd look at the voltage where the waveform transition occurs.

If below 13.5V (assuming a 12V battery), I'd suspect the regulator.

If around 13.5V, the regulator is probably doing it's job (even if it looks like 1/3 of the SCRs is firing) and I'd check alternator coupling to engine.

My money would be on the regulator.