Corrupt EXT partition on SD card?

[Guest sooee]

I installed the new update to the Facebook app today on my rooted desire (running the r5 ROM from here) and I think it killed the battery life in my phone because it ran out a full 6 hours before normal on my way home from work today. I don't think the phone shut down properly because when I got home the phone wouldn't boot (kept looping on the HTC screen)

Tried a factory reset/wipe/reinstall ROM etc and nothing worked. I cooked a new ROM on here without Apps2SD, installed it, and the phone booted. So I think I have a corrupt EXT partition on the SD card.

Have eventually got everything working so I am trying to do a nandroid backup but it's stuck at about 95% backing up lost+found... it's been stuck for about 10 minutes and I don't know what to do - think I'm gonna have to pull the battery but I don't want to brick my phone again!

Eventually I want to reformat my card to get rid of the EXT partition - do I have to use ROM manager for this? I'm guessing I can't pull the card and reformat it in my PC because it can't see both partitions?

Any help/advice much appreciated!