About the first problem, is the first time that you have the scenario in the QA or you have done previous transports?, have you check that in your develop system had all the object activated?,
This is first time transports and I changed and activated objects before transports ,also in QA I changed activated with PISUPRER.
have you tried to modify all the object in dev enviroment with a dummy change, like change the description, activate all its ESR objects together and transport again?.
Yes
About the cache problem, could you check if this note is appliable to your system?: 1638667 - PI has wrong Usage Type setting after SP Update, the exception point there is similar than yours.
I checked this note and already our system having same defualt values as recommended by note