This is by design - I do agree that it's a bit odd way of doing it. Especially considering that it's extremely hard, as far as I can tell, to switch off encryption for the ReadyBoost.
Reason for that behavior is, that ReadyBoost cashe is encrypted with a single use key that will be flushed when you reboot. So after the reboot a new encryption key is generated and thus a readyboost cashe has to be refilled again.
I do know that this can be switched off somehow, but the process of doing that is very uncomfortable. What you basically would be needing to to is to build OEM scripted windows installation package for your specific hardware configuration and then switch off the encryption/compression in the hands-off-installation script. I have been trying to find a way of doing that without having to reinstall but have not found a solution yet. Microsoft specifically emphazises in their documentation that OEM scrip installation tools should NOT be used on already deployed system, although I'm willing to give it a try. Just have to find a way of doing that.
I assume that all it does in reality is adding some specific registry keys somewhere. When I eventually get around doing the scripted installation tingy all I would have to do afterwards would be finding the registry keys and importing them over to my main system. Or at least thats what I hope.