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So after the Wubi finished the install and rebooted, something failed and went to busybox shell. I have tried this twice now.

System Specs:

I7 930 OC 4.21 6GB DDR3 1600 Mushkin Blackline C: WD Raptor 300x2 RAID 0 D: WD Blue 250GB (Apps) E: Seagate 320 GB (Movies) F: WD Black 750GB (Movies)

Is the RAID breaking my Ubuntu install or something else?

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I think(note think, I'm not sure) that Wubi has an issue with RAID. Your question does not specify but if you are using WUBI with anything newer than 12.04 it is no longer supported by WUBI. WUBI aslo, I believe, cannot support EFI. So any of those could be your issue. –  TrailRider Dec 8 '13 at 22:08

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