Hi Julian, thanks for your suggestion. Having played about with some kitchen foil to confirm the frog is the issue (rather than the closure rails or switch rails), I am thinking along the same lines as yourself.
I believe what is happening is that at very slow speed the loco wheel is 'dropping' off the V of the frog causing one or more of the other wheels on the opposite stock rail to rise slightly and lose electrical contact, when the loco tips slightly towards the frog. Using a test wire between stock rail and those wheels re-establishes contact and the loco starts moving again
This reminds me or something I forgot to mention earlier.
Uneven passage across a crossing V isn't necessarily the V itself protruding upwards. It could also be the wheels dropping into the V which is what you appear to have identified.
There are a few ways of dealing with this:
1) Dropping into a crossing is often caused by the back-to-back measurement of wheelsets being less that what they should be. They should be 14.5mm for 00 scale. Try correcting the gauge (not always easy on locos), but at least you should check it.
2) Similarly, the gaps between rails and the depth of the crossing also have an impact. As others have already indicated, SetTrack is a 1960's/70's phenomenon, designed when steam-roller wheels were all the rage and deep flanges were fitted to match. SetTrack and Peco 'universal' was designed to be compatible with this and still is, consequently, the tolerances on check rails and crossings are way more than what they need to be for modern stock.
I suspect you may be running relatively recent stock on 1960's standards track and this is why you are having problems.
3) Insert a shim of plastic in the bottom of the crossing. The purpose is to allow flanges to run along it instead of dropping further into the V. Peco actually do this on their 7mm scale turnouts. It's not my preferred option as gauging wheels normally fixes the issue, but if it works for you, it may be a way to go.
I recall about 20 years ago, taking my rolling to stock to run on someone else's layout. My layout is Peco code 75 and wheels are gauged to match. Perfect running all the time and still is. The other person's layout was SetTrack. Needless to say, my stock spent more time off the rails than on them. It was a waste of time trying to run decent models on crap track.
Set Track really should be confined to the bin. It isn't suitable for modern models and this is why we have things such as the code 75 and bullhead track ranges which are way better.