You're saying that both discs are actually disc 2, though one of them is labeled disc 1? That's messed up. Is it for Dreamcast, PS2, Gamecube?
Do any versions of it besides the Dreamcast even have multiple discs? I know the PS2 version is single disc (unless you count that it came with a Devil May Cry demo disc, but who would count that). Is the Gamecube version multiple disc?