I was debugging something very similar to this at a customer just the other day. Turns out the sourcetype renaming transforms rely on there being 3 CSV fields before the log type field (THREAT, TRAFFIC, ...) whereas the customer's logs only had 2 (received_time and serial_number). You might want to check if this is the case in your setup as well. If so, the fix is to remove one of the groups in the transform in transforms.conf, so for instance the traffic log transform would change from this:
[pan_traffic]
DEST_KEY = MetaData:Sourcetype
REGEX = ([^,]+,[^,]+,[^,]+,TRAFFIC,)
FORMAT = sourcetype::pan_traffic
to this:
[pan_traffic]
DEST_KEY = MetaData:Sourcetype
REGEX = ([^,]+,[^,]+,TRAFFIC,)
FORMAT = sourcetype::pan_traffic
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