[Milhouse]

Can you try copying the files from FAT partition off the sdcard, formatting it (which should be safe, windows won't touch the ext partitions), and copying back on (and checking they are identical to expected ones).

EDIT: could you backup the sdcard (with dd/winimage) first. Just in case my suggestion fixes it, it may be interesting to analyse the FAT partition.
I have a suspicion that when FAT parition gets sufficiently defragmented it may provoke a bug in the bootcode that stops it booting - but that is not proven.

I took a backup of the entire card (~100MB .tar.gz - working on setting up a dropbox account and will PM you a link), plus the files that are on there. It's a 4GB Class 4 SD card, but only contains a single 3.75GB FAT32 partition as I'm using NFS for /storage.

I analysed the fragmentation level in Windows, and it was 0%. I compared the files that should be on the card, with what are actually on there, and there is no difference so it looks like the integrity of the files is fine.

I performed a Quick format (FAT32) in Windows7, copied the original files back on - no boot. Compared the files, still no differences.

I performed a Full format (FAT32) in Windows7, copied the original files back on - no boot. Compared the files, still no differences.

I then reformatted the partition using mkfs.vfat in Ubuntu 13.04, copied *new* files extracted from a git build (which works on other cards) and still no boot!

And when I say "no boot", all I get is a steady red light as soon as power is applied, no other LEDs are illuminated, not even briefly.

I'm happy to post this SD card to you if you wish to receive it - PM me an address!