Could be many things, DNS, bad packets etc. You probably have to use a network sniffer to find out what causes the timeouts. I still think it is coincidence that the server browser experience has changed with the upgrade. Maybe something else happened at the same time?
I guess you have already seen this KB (as you have already changed scalable http):
KB23933-After a BlackBerry Enterprise Server update, BlackBerry smartphone users are unable to browse to web sites