According to our traffic logs a lot of traffic is denied during a period of 15-20 seconds every time we update applications and threats on our PA-5050. Is this normal? This is all kinds of traffic like mssql-db, web-browsing, ms-sms etc.
No, that is not normal. Seems like you have either a bug or some kind of network issue at play. If you don't see any connectivity reason (half duplex ports in the path or other layer 3 problems) I would open a ticket with support to investigate.
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