Hello Again @Jack
I have a spare MX100 running 12.24 that I reset back to factory and I enabled AMP and IDS like you have, see screenshots. I also added the L7 rules you mentioned above. I happen to have an extra connection to the outside world with a public IP, so there is not a double NAT taking place here. I had no problem fetching updates from windows update servers or adobe updates. if this traffic was getting grabbed by IDS or by AMP, there would be a log of that event that is easy to find the in security center.
This very much sound like an issue with Content Filtering, more specifically IP/URL reputation as @PhilipDAth mentioned.
"In firmware version 13.3, URL reputation was prioritized over IP reputation, as opposed to IP reputation being the deciding factor on previous firmware versions. If, for some reason, the IP has a different categorization then the URL, the client could be allowed through."
I can tell you that I am running MX 14.15 on an MX250 and I have not been adversely affected by this beta firmware in a production environment with 1000+ daily clients.
"If a client is being blocked from accessing a page, the easiest way to tell whether content filtering is blocking the traffic is to check your Event Log. When looking at the Security Appliance's network in the dashboard, navigate to Network-wide > Monitor > Event log. To help narrow down the scope, the event type 'Content filtering blocked URL' can be included in the 'Event type include' field."
I hope this helps.
Ryan