Since neither Windows nor the camera can read the card, I think the most likely scenario is that the changes Windows were about to write to the card were interrupted halfway through.
Such interruptions will corrupt a file system for sure, and could happen if you just unplug the card instead of going through the Windows "safely remove hardware and eject media" option. (In the bottom right of the desktop, it pops up whenever you plug in a USB device. You may have to click the upward pointing triangle/arrow, with the "show hidden icons" mouseover text, in order to see it.)
Or it could happen if you suddenly lose power to the computer in the middle of a write.
The problem is that when you make changes to a storage device (hard disk, memory card etc.) the operating system doesn't write these changes to the device immediately. Instead the OS will wait a bit to see if there are more changes coming, so it can write out several changes in one go, which is much faster than doing the changes one keypress at a time. So the last few changes stay in the computer for a while, and aren't finalized (written to the card) before either the user or an OS timer requests it.
Corruption happens when the OS has started to write changes, but didn't get the chance to complete it. This can (will) leave the file system in an illegal state that cannot be read by anyone, aka corrupted.
If you have a corrupted card, the best chance to recover anything lies with a file recovery program. Some of these programs will work even if the file allocation table (the "table of contents" that tells the computer/camera which files are at which storage locations) is broken, although they may recover some garbage in the process, and some files may not be recoverable.
The simplest way to avoid such problems in the future may be to delete only through the camera menu. But as long as you do proper synchronization ("safely remove hardware...") there shouldn't be any problems. In theory.