How are you looking for your deposits? Coming from your original wallet address? Did you check to see if maybe one of your "change" addresses is listed instead? A new change address is generated for the leftover "change" from an input instead of sending it back to the originiating address. So next time you send coins somewhere, it will take inputs from your change address for transactions.

I had missing deposit as well until i looked for the change address the second time i deposited coins there.

You can enter "listaddressgroupings" in the wallet debug console to list all your addresses and their balances.