I bought a 16gb SDHC card a couple of months ago. I filled it up with music and it seemed to work fine, but then I noticed that some albums I thought I transferred were not on the card. So I put the card in the card reader built into my laptop and tried to transfer over the music again. I can't remember the exact order of events, but it went something like this.

1) Transferred music over
2) Noticed that although the properties for the SD card said I only had 11gb on the card, the Music folder on the card said that it was 90gb.
3) Saw that there were two folders that said they were 30 and 50gb or something like that and Windows wouldn't let me delete them (file name too long)
4) Ejected the card and tried to play in my N800 and got an error message that the card could not be read, and do I want to try and repair.

Since then I've ended up reformatting the card a couple of times (have to do it in N800 as Vista spends 10 minutes or so formatting, gets to the end, and then says that it could not format the card.

I've now been retransferring music folders one by one to the card, it seems like everything is transferring fine (i.e. it takes a couple of minutes per folder, usually 100-300mb) but then I checked a number of the folders I transferred were empty, the folder structure was there, but no files. For other folders it looks like all the files transferred, but some of them are missing tag data that is in the original file.

What's going on, do I have a bad card?

Do you safely eject the card each time?

Anyway, if I had a problematic card like that, I might try "sudo dd if=/dev/name_of_card of=/dev/null" in Linux to read the entire card and watch for errors. I'd also check the system log for info (this might help in Windows, too). If that didn't help, I'd move on to write tests.

OS 2007 on the N800 had a bug that ate SD cards. The latest version of OS 2007 is supposed to fix this, and OS 2008 shouldn't have this bug anymore.
I once lost a 2GB card with OS 2007. It showed read errors, and no matter how often I reformatted it, it was always showing the same files. dd on Linux didn't help either.

I'm running 2008 and have the entire time I've had this card, so hopefully that isn't it.

I just was copying folders back over 1 by 1 and checking after each folder to see the size. Everything seemed to transfer over fine, but then a folder I'd checked that had been about 100MB, is now showing as larger than 25.6GB. Another folder is now empty that had previously had files on it.

I do safely eject each time from Windows (one time the card wouldn't eject, so I closed everything and shut down the computer and then ejected).

I checked the System Log, but didn't see any obvious errors, everything for the last week or so was a DHCP error.

I'm not a linux guy and my knowledge of the command line in Windows is limited at best. Is there anyone who could walk me through what I'd need to do to test errors on the card from Windows?

Your card is hosed. Even if you manage to make it work for a while I would never trust a card like that with any important data. Save yourself a lot of pain and try and get it replaced under warranty.