Hi MXphile,
Welcome to the posters club.. lol.. just kidding.. welcome to our forum.
I have heard a few people having this same troubles as you however, its been an issue since way before the crash took place.
Let me reassure you about the PIE Patch the best I can. They do not have the caches they control set up to ignore *.dll users at this time. Those are concerns of ours for future developments and why we are watching things closely.
The secondary connection problem is not easy to solve, I am connected secondary and find this happens to myself also from time to time but usually exiting the program completely and restarting it seems to help as a temporary solution. This can be aggrivating indeed, and your observations are the same as my own regarding the search resutls . It appears to have lost its connection before it even knows it, this could be attributed though, to the primary your connected through.
I suspect that if its due to a stressed primary connection, usually related to the flooding, that things should get better with time and more users coming back.
Ok long winded and not many answers its true, your concerns are valid, your not alone, so its more then likely not your system or set up, and for now just restart is my best advice.