We're having the same issue. We're still on 9.32, thinking about upgrading today.
We have roughly 1200 users that should be scoped similar number of apps (19), we had 820 licenses to the paid ones initially, which took over a week to fill out in the JSS. The JSS is now reporting that all those licenses are in use, but many students who have been "assigned" those apps according to the JSS do not have them in purchase history. We also bought 450 more licenses for padding and those have yet to appear as available in the JSS despite being listed as "managed purchases" in Apple's account history on VPP site.
In testing over the summer, enrolling a few devices it maybe took 5-10 minutes at most to see those apps appear in history, but apparently throw all those users and app assignments at once and something hit a hiccup.
Hoping 9.4 helps. Apple also suggested re-importing the VPP token, but I don't get what was wrong with the other token if some people were starting to get apps.
If it helps, our apps are assigned by IDing a user based on email address, as our students have a subdomain in their email so I can easily scope them to get a specific set (we didn't have AD groups in place before the scoping took place), and I have two app assignments, one with free apps (12 checked off) and one with paid (7 checked off).
