We bundle a Java runtime (except for Linux) to minimise the software dependency.
Things like system clock time etc aren't used for the encryption.
It would be interesting to see that wallet data to see if there are any clues to what went wrong. It does sound like a bug that is happening infrequently so it would be worth following up on. Bugs like that it is quite difficult to get good data on so your wallet would be quite useful.
First thing to do: get your bitcoins out without disturbing the wallet by either using another machine or downloading Lighthouse (https://www.vinumeris.com/lighthouse), use your wallet words to recover the wallet and then empty it.
If you don't mind me seeing the wallet data the best thing for forensics would be a zip of the whole wallet directory that you send to me.
I can then trawl through all the logs and backups etc.
If you do this NEVER USE THAT WALLET again - it will be totally compromised as I will have seen it.
You can see the wallet directory if you go into the Manage wallet | Wallet dashboard.
Navigate to the directory then close down MultiBit HD (so that it writes everything out) and then zip the directory.
Then pop it on somewhere like dropbox and email me at j i m 6 1 8 @ f a s t m a i l . c o . u k
+ the dropbox URL
+ your wallet words
+ your wallet password
Just to repeat - never use this wallet again !
If you do not want to do this then a zip file of the log directory would be fairly useful (though not as good). It is in the same directory as where all the very long wallet directories are stored.
The logs do contain transaction data but no notes or anything so contains less private info.
If you aren't happy to send me either of these for privacy reasons I won't be able to find out anything more - that is totally your decision.
I will give you the logs. I have not decided if i wish to completely change all my addresses, specially since i used some for signed message verification. But when i have decided i will let you know.
Check your emails.