Just making wild guesses, not having really had the chance to ever work on one of these yet...
The HV circuit is clearly a free running tuned RC circuit run from main bias with a tie to the AC line, assuming the 2 HV caps were replaced, (500pf?)
And guessing that other caps / resistors in the area were also changed with newer kinds, and this all could perhaps change the resonant frequency of the HV circuit, or overall behavior which could possibly include the proximity of the CRT to the chassis, and the parts in it.
IE, starting some kind of weird feedback loop that just won't break.
But, as stated, this is just a guess!