Aren't POS mined coins from Masternodes supposed to be valid after 188 confirms? Everything I have staked with Masternodes is "missing" from my wallet, I have the same balance.
The full amount of the stake is shown, but after it confirms when you close the wallet and open again you will see only the MN portion accredited to you. This is normal.
PS: I think you are doing something wrong with your MN setup. They seem to work as designed.
My block rewards were coming across with incorrect values, that's why it wasn't adding up. I .old'd my appdata directory dropped my conf and wallet file back in and resync'd. That fixed the values. Back to Masternode staking.