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It's an option in TWGS that can be enabled/disabled.
Nod, called ship delay (or move delay). It's a system-wide option, instead of a game-specific option, which has spelled it's death. To add to the problem xport, tpad and pwarp have no delay, while typical moves and attacks do. This means someone w/ a pwarp foton script can almost certainly hit you, and you've got no chance to escape. Ship delay moves the game even further towards planet-based play. There was some talk this might be changed, adding a delay to planets as an option and making ship delay game-specific instead of server-wide... if that ever happens we might see a resurgence in ship delay.
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As for keeping my ports list up to date . . . is there some system script that records that and creates a list that I need or what?
Depends on what you want to specifically do. A lot of CIM hunters do frequent CIMs and then compare 2 CIM results and act accordingly. What you asked for was different, you want something that can compare against your database and not just against an immediately previous CIM. That's a big difference.
There are no public scripts for TWXproxy that I know of that can do this, but it's not hard to write one. Earlier someone said Swath can do this, so maybe that'd work instead.
Provided you've been running TWXproxy most of the game, all you need to do is run a CIM ever-so-often as you play to keep your DB up to date. Ports that don't show up in the most recent CIM will have update timestamps less than current, so all you need to do is write a script to check timestamps for every port.