So, at Fiskbit's request, I tested both my Magic John and Lord of King carts (same developers) on my modified front-loader. Both of them initially boot fine, BUT if you either press Reset or cycle the power too quickly, they freeze at a black screen. Holding Reset does not work; the console must be completely powered off to get them to boot again. The amount of time required between power cycles also varies slightly between the two:
Magic John: 5-6 seconds
Lord of King: 4-5 seconds
I also tested the games on my AV Famicom and they booted normally every time, regardless of how many times I pressed Reset or power-cycled the console. I also have a top-loading NES, but don't currently have a way to hook it up (I need to dig out an RF box).
[UPDATE]
I really need to organize my closet
I tested Magic John on the top-loading NES, and it exhibits the same behavior as the modded front-loader w/r/t power-cycling (need to wait 5-6 seconds between attempts); however, pressing Reset
does allow the game to boot, presumably because the PPU has warmed up by this point. So the question is, why does the top-loading NES behave differently from the AV Famicom? The only real difference is that my AV Famicom has rev. H CPU/PPU, whereas the two NESes both have rev. G. But if the game works properly on older Famicoms, wouldn't that rule out CPU/PPU revisional differences? I'm confused.