VPP Mobile Device Apps not showing in the list

What I do in your situation is to add then via the JSS.

In the mobile device app section I click on the '+' symbol (New) then through that I "Add" the app I bought.

This talks with the iTunes and VPP store so it kind of "Pulls" the app down from Apple rather than a "Push" which if you're using VPP store you are doing.

What anickless is proposing is working! When I recall these bugs in JAMF I use to switch from Firefox to Chrome-browser and add these apps manually.

Shouldn't apps synk automatically to Mobile Device Apps after purchase?

Apps will only automatically show if you have "Populate Purchased VPP Content" selected in the VPP Account. If you don't you'll have to manually add each one to populate.