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I did wonder when you mentioned you have a V4. There were a few different flavors of V4 and some of them seemed to be a bitch about certain things. For example, when no-swap mods were first coming out, I ordered a premod console from lik-sang (back before they got sued, heh). What I got was a V4R that I discovered would never pass DNAS checks with online games, even though I verified that the sleep mode of the chip was working properly (this was before dnas patching.)
Putting the same NA and HDD in another machine and having it work makes me wonder if you just have one of those quirky consoles. I know you don't want to hear "get another PS2", especially these days when the older non-slim models are getting harder to find, but that's just what you may need to do.