All Quartz Blocks and Wool blocks (no colour) disappeared after updgrading to 1.6.1

When we upgraded our launchers (1.0.8) and server (1.6.1) last week, now all of the quartz blocks and wool (only the default wool colour - coloured wool blocks stayed in place) we had placed had totally disappeared, you can walk through and place new blocks in the space where they used to be. I though maybe the light colour might be causing problems with the video card or something, but you can build the new blocks, and the new ones have survived multiple restarts. I have tried reinstalling Minecraft on the server, and the launchers, multiple times with no success (and restarts obviously). We also upgraded to 1.6.2 with no success either.

Please help, we're looking at hours and hours work to rebuild!