Actually, no, it doesn't. You played live with your 250 gig, and after you took it out, you were banned. They detected that you had it, and once you put your stock back in, i guess they finally went after you since today is Halo 2 aka mod dooms day.
Also Veryn, you seem to be getting it wrong. You get an error when booting up an xbox with a motherboard with a mismatched hdd and motherboard eeprom. there is no way you can play on xbox live even if you mess up with the eeprom flashing, since your xbox won't even boot then. If you have an unbanned eeprom, and you are using a stock hdd with the chip off, you should be fine. Thats the reason that hdds and motherboards are sold in pair, because you need a matching set in order to get your box to boot in the first place.
AvramE