It seems that the network forked, we are still early in development with no serious resources allocated so things are moving slow. They will move significantly faster now.
This is not a surprise at all. Anyone who compared 0.0.0.4 and 0.0.0.5, and who also has some background in cryptocurrency implementation, would see that the patch that was applied would be highly likely to lead to forks. It seems unlikely that it wasn't known before releasing 0.0.0.5 (unless the developers were hobbyists, but that seems out of the question - I read something about a brilliant team of engineers being involved).
How should users proceed whose transactions are not included in the blockchain available for download? Overwriting the consensus-generated blockchain created by the wallet client by the one crafted by the developer team might lead to loss of balances, so I assume the losses can be compensated somehow.