I am also plagued by that exact same problem but I'm not sure this is the reason for my issue since I tried the method suggested and left Agama running for over an hour to no avail.
I believe the other alternative is that I might have asked for my KMD to be sent to a different address. I just read about how Agama might in some instances give you two separate deposit addresses but only one is the correct one. If this is the case, is there any recourse for me or are those coins lost in the ether forever?
FYI, I used Shapeshift to exchange Litecoin for KMD. The Litecoin was sent from my Electrum wallet.
Check the address balance here :
http://kmd.explorer.supernet.org/If it shows up above then you should be just be able to do "Basilisk actions" -> "Clear cache and fetch wallet data" -> takes a minute or two to update the balance.