I just took a quick peek at the TA, and it looks like it expects the initial sourcetype to be pan_log (or pan:log). Are you setting yours to just pan in your inputs? That might explain why it's not getting processed correctly
[pan_log]
rename = pan:log
pulldown_type = false
# This first line adjusts PAN-OS 6.1.0 threat logs to revised 6.1.1+ format where the reportid field is at the end.
SEDCMD-6_1_0 = s/^((?:[^,]+,){3}THREAT,(?:[^,]*,){27}".*",[^,]*,)(\d+),((?:[^,]*,){3})(\d+,0x\d+,(?:[^,]*,){14})$/\1\3\4,\2/
TRANSFORMS-sourcetype = pan_threat, pan_traffic, pan_system, pan_config, pan_hipmatch, pan_endpoint
SHOULD_LINEMERGE = false
MAX_TIMESTAMP_LOOKAHEAD = 44
[pan:log]
category = Network & Security
description = Output produced by the Palo Alto Networks Next-generation Firewall and Traps Endpoint Security Manager
pulldown_type = true
# This first line adjusts PAN-OS 6.1.0 threat logs to revised 6.1.1+ format where the reportid field is at the end.
SEDCMD-6_1_0 = s/^((?:[^,]+,){3}THREAT,(?:[^,]*,){27}".*",[^,]*,)(\d+),((?:[^,]*,){3})(\d+,0x\d+,(?:[^,]*,){14})$/\1\3\4,\2/
SHOULD_LINEMERGE = false
MAX_TIMESTAMP_LOOKAHEAD = 44
TRANSFORMS-sourcetype = pan_threat, pan_traffic, pan_system, pan_config, pan_hipmatch, pan_endpoint
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