I've also run malwarebytes and hitmanpro and there's no known malware running on my PC
FTFY.
Is this wallet on a machine which is used for browsing normally? If so, it may be malware which has not been caught by anti-malware services which has stolen your wallet.dat or private .key files. If the transaction is being shown as confirmed on block explorers such as
Blockchain or
Blockr there is no way of you getting those coins back, no matter whether you re-sync the blockchain in your wallet or not.
Obviously, I'm assuming you haven't given away your private keys to any service, or used any service which generated the private keys used for that address.
From here, I suggest that you make a new wallet on an
offline, formatted computer and send any coins you can't afford to lose there. Do not connect this computer to the internet unless it is completely necessary.