Here are all of the changes in the various patches.
1.029
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now handle dropping fragments of connect, connect response, and first server data much better
now save fragments instead of dropping out of order fragments
no longer send client data before getting first server data
now limit first few frames data rate from server a little less (5000 instead of 2000)
increased receive and send udp buffers from default to 100,000
increased max fragment start offset from 16 to 24 bits
now should handle packets that end exactly on the fragments size boundary better
changing missing base in database stuff from a critical error to an error (getting random errors before version error)
missile defense will now shoot at station missiles (Crusender) (IotA)
marines can no longer board devices and space objects (IotA)
now show Trade Pacts when highlighting race icons
increased scavenge costs from 125.0 to 150.0 (IotA)
increased trap damage by 50%
doubled trap delay
no longer show green + on classified components
removed mandatory quest warning from prevent wins, must win types, and win timer Drox quests (IotA)
changed greenlight button color (Steve)
fixed Damage not being localized correctly (DarthNihilus)
rewrote prevent legend win text a little (IotA)
fixed difficulty localization in highlight text on Create New Sector button (DarthNihilus)
added n_printMessageNames for debugging network stuff
changed PROTOCOL_VERSION to 28