Okay, I think I figured out what the problem is. Actually, there's two problems.
1) You had logged out into the hardcore world and remained there since the update. I don't know what happened, but the HC world is almost completely inaccessible. This is going to take time to figure out and fix. I should be able to restore your inventory, however.
2) There has been some damage and reversions done to a number of chunks. I'm not entirely sure how many were changed and reverted, but the most obvious was Josh's structure around his nether portal. Presumably, there's probably been some reversion of things inside the normal world's nether, but I haven't yet checked. I've selected most of the areas I've known that Josh has altered and replayed the LogBlock log to restore everything, including his chests (their contents reverted back to sometime before the 11th). Everything is mostly back to normal, but I'll have to get him to verify this. If not, then there's a bit more work to do.
So, if you've been on since the 10th or 11th, your work may have been reverted in whole or in part. I'll need to fix this manually. What puzzles me the most is that this isn't the first time I've heard of this. Cosh mentioned that an area he had been working in appeared to completely revert (ore included), and I attributed it to something of a fluke. That means that this is the second time such a reversion has taken place, and both reversions have occurred in chunks that were first generated in 1.8 BETA (!) and recently changed (within the last month). Perhaps it's a coincidence, but none of the work I've done in chunks that have been generated only a handful of weeks ago appears to be reverted. Elade's area appears unaffected, too, which suggests that the actual damage may be isolated to a relatively small period of time (about 2-3 days).
I honestly have no idea what caused this problem. I can only speculate that it may be due to the Java process crash/freeze, but I don't have enough data to verify whether or not that's the cause. Bukkit isn't using the same save methods that the stock Minecraft server does, and I have no idea if that could plausibly be interfering (I doubt it, but it's almost acting as if save was disabled somehow).
Anyway, I apologize for the issues. I'll see about restoring your inventory, Ralph. It should be pretty straightforward given the backups and may or may not catch everything, but the best bet is for you to camp out in the default world for now. Your inventory there looks like it should be intact.
Sorry. I'm afraid I don't have the instrumentation available to me to be able to determine exactly what has happened.
If any of you are affected let me know, point out the areas that have been damaged, and I'll do my best to replay the logs on them.