Do NOT edit things in etc/system/default. Those are default values, not meant for local changes. For local changes, use local rather than default. https://docs.splunk.com/Documentation/Splunk/6.6.2/Admin/Configurationfiledirectories
What you describe - tcp port rather than splunktcp port - is exactly what's causing the indexer to not treat the cooked stream as cooked, and instead to index it as-is.
turn off all tcp inputs you use to recieve data from forwarders (settings -> data inputs -> tcp)
turn on receiving for those ports (settings -> forwarding and receiving -> configure receiving)
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