Mini-tutorial really, but the problem occurs in a number of servers.
After searching and asking about this over Christmas, Bejaymac provided the key to unlocking the problem of bases not appearing in the trade window after you have visited a base.
I am presuming that you have added the bases and systems so your universe.ini and system.ini's all have the correct entries and IDS etc. With bases listed before systems.
In particular strid_name in Universe.ini and ids_name from the respective system ini should match.
You then need to edit the InfocardMap.ini which is composed of two columns
First column is the ids_name from the system inis and should match the strid name from Universe.ini
The second column is the number of the infocard for that base.