I have had my VOM for a couple of years. I went back and checked, it does measure square wave voltages. That's why I bought it.
I didn't say your meter can't measure square waves. I said it can't measure variable frequency square waves
accurately. RMS meters (except ultra expensive heat method meters) measure square waves accurately only when the square wave has a 50% duty cycle which DCC does not. The meter measurement accuracy further degrades as the frequency of the measured wave nears or exceeds the meter's sampling frequency. The frequency of a DCC wave is in constant flux due to the pulse information being conveyed. It can and does change during your meter's sample period. Add to all this, most RMS meters AC couple the signal which causes further inaccuracy. Long story short, a scope is the only truly accurate way to measure power (voltage under load) of a variable frequency square wave. Here is a video that explains a lot although it stops just shy of getting into variable frequency PWM.
https://www.youtube.com/watch?v=ue0wtlrmCJENevertheless, the inaccuracy in your meter is the same during both measurements so it is still a valid indicator there is a voltage drop.
Two #16 THHN wires in parallel have a capacity of 36 Amps, more than a single #12 THHN. A few years ago I picked up a 500' roll of red and a 500' roll of blue for $20.00 each. For me, it was much easier to run under the layout and to twist the two colors together to try to eliminate crosstalk. I use brass shorting bars for connections.
Point of clarification. Ampacity ratings are given based on the ability of the conductor and insulation to manage heat generation. As an example note the difference in ampacity ratings for the same AWG of THWN vs THWN-2. Ampacity ratings themselves do not take into account run length and resulting voltage drop. They are simply maximums for safe operation.
Since you reference 12AWG while in my reply I did not, I am going to assume your read my blog. When I wrote "wire your layout correctly" I did not say use 12AWG. By wire correctly I mean use a wire of sufficient gauge such that it will not exceed your personally set limitation of maximum allowable voltage drop under the maximum load at the furthest point from the power source. That just happened to be 12AWG in my particular layout situation.
If we assume your 16AWG wires are not exceptionally long and we assume your termination methods are of adequately low resistance then the evidence points toward the DCC booster or power supply. It could be sloppy voltage regulation in either component, a result of the DCC signal waveform being broadcast, or a combination of both.
Want predictable voltage levels? Ditch the DCC stuff and use a high quality switch mode power supply preferably one with remote sensing. Or, quit measuring and enjoy running trains!