A friend of mine bought about $2000 worth of Bitcoin a couple of weeks ago and (despite my advice to transfer it to his wallet) left it in his Mt. Gox account. A couple of days ago, the Bitcoin and his transaction history completely disappeared from his account. No response from Mt. Gox yet.
There have been numerous threads on the forum with titles like "MT GOX RIPPED ME OFF!!11" but every time the problem was dealt with quickly and pleasantly by MagicTux. He's very well respected in the Bitcoin community and I'm sure the MtGox team will do whatever they can to fix whatever went wrong. Clearly they're reached a new level of scale these last few weeks, so perhaps the latency of response has slowed.
Have you tried contacting them on the Bitcoin forum or IRC? Or perhaps send another email.
It would surprise me if Mt. Gox would maliciously manipulate accounts, as this would not make sense for them. Currently they own loads of money via transaction fees - why should they risk their monopoly status for some short term gains?
Perhaps because they think that there are only short-term gains to be had out of bitcoin? I'll take a hundred thousand real dollars now over a million bitcoins in 2013, thankyou very much.
MtGox has been fundamental to the whole pump-and-dump side of bitcoin so it wouldn't surprise me if they're manipulating the market.