I'm not sure the root of it off hand, this is the piece it is referring to as the Stake modifier.

// Get stake modifier checksum
unsigned int GetStakeModifierChecksum(const CBlockIndex* pindex)
{
    assert (pindex->pprev || pindex->GetBlockHash() == (!fTestNet ? hashGenesisBlock : hashGenesisBlockTestNet));
    // Hash previous checksum with flags, hashProofOfStake and nStakeModifier
    CDataStream ss(SER_GETHASH, 0);
    if (pindex->pprev)
        ss << pindex->pprev->nStakeModifierChecksum;
    ss << pindex->nFlags << pindex->hashProofOfStake << pindex->nStakeModifier;
    uint256 hashChecksum = Hash(ss.begin(), ss.end());
    hashChecksum >>= (256 - 32);
    return hashChecksum.Get64();
}

It will fix the problem to move your wallet out of your roaming folder, delete the Blockchain and resync and then once fully synced, to replace the empty wallet with the one containing your balance. I'll update the bootstrap and full Blockchain downloads when I wake up, is there anything you did differently?