If it helps any, Im running:
120Gb HD, (The bios on the chip is whatever X2 one was the first to block XB Live connections), Xecuter 2 Pro
C Partition: Stock xboxdash.xbe, UnleashX named as evoxdash.xbe, Skins folder in root of C for UnleashX, SDK Software (For which yes, I am a valid user)
E Partition: Additional SDK Software, Homebrew Apps, Folders used by Emulators
F Partition: (Movies, Games, ROMs, stand F drive usage stuff)
I have played on Xbox Live nearly daily with Halo 2 and have yet to be banned. this leads me to believe (and this is probably already discussed) that:
A ) Non-stock HD isn't causing the bans.
B ) Having non-stock files on the HD isn't causing the bans either (Unless these non-stock files overwrite stock ones, as someone suggested before)
C ) LPC scans are not being performed.