As an experiment try taking out one or two of the board returning good results and see if that changes anything. Unpowered hubs do have some problems as any current taken will multiply up with the number of boards. It doesn't take much to overload an unpowered hub. Powered hubs are definately better and I would suggest this as a good thing to use for the short term
One other general issue with USB is that the way it timeslots data can mean that the USB can run out bandwidth on relatively low bandwidth applications e.g. serial coms with a relatively small number of boards. I would be surprised if 5 boards caused this issue but I am not an expert in USB protocol so I can't be more specific. It can be worth spreading your boards aroung your PCs ports. This isn't always a solution as an occasional PC has an internal hub for multiple ports which only actually has one USB controller but for most PCs this is a good way forward. Once we get the up/down function sorted out these potential USB problems should more or less dissappear.
Ok, I will try this a bit later, once I figure out which board it is, Would you care to comment on why the boards only work in usb3 ports for me ?