May I ask, how did you make the changes? The game comes with an editor, which is the file called SupremacyEditor2.exe. You should use this to make changes - don't manually edit the game files as this may cause problems.
You may have also noticed that there is a SupremacyEditor3.exe file - this IS an updated version of the editor as it sounds, but do NOT use it; this version of the editor is incomplete and still under development.
Anyways, if you have been using the correct version of the editor to make the changes, make sure that you close the editor - and SAVE THE CHANGES - before you load up a game. Also, once you have made changes, don't load up a game that you've previously saved as this may cause incompatibilities and bugs. You will have to load up a new game and start from scratch. You must also stop the game from performing updates - if it asks whether to do so - or your changes will be lost. There's an option to turn the auto-updater off in the game menu, or you can just manually cancel it each time it comes up.
You are correct about the efficiency rate; this is what tells the game how good a shipyard is at building a ship. The efficiency is the percentage of system industry is chanelled into ship production - so if you have a system producing 100 industry and a shipyard with a 25% efficincy rate, 25 industry will be put into shipbuilding. This industry is NOT taken away from building structures though, so technically your industry gets doubled up...anyways, the game should remember the changes that you make as long as do the things I mentioned above; save the changes, start a new game, and don't let it perform an update. However, changing the output of the research and industrial facilities should NOT have any effect on the efficiency rate of the shipyards or any other part of the game, so either you accidentally made other changes, or you loaded up an old save game and this resulted in incompatibilities.
I'm personally working on a content update for the game, which includes some major changes to the stats and prerequisite/upgrade/obsoletion paths for the shipyards. I can't remember whether I made any changes to the efficiency rates for the Klingon shipyards, but I just checked and they do have the correct rates set in my files. In fact, Klingon shipyards are more efficient than Federation shipyards because they have a 30/60/80 efficiency rate, as opposed to the Federation's 25/50/75 rate.
100% efficiency rates are reserved for only the very biggest shipyards; the Fleetyards (Cardassian Union Fleetyard, Dominion Attack Fleet Construction Facility, Federation Starfleet Advanced Fleetyard, Federation Utopia Planitia, Klingon Imperial Fleetyard, and Romulan Imperial Fleetyard) and the minor race special structures (Shipyards of Axanar, Kazon Shipyard, and Tellarite Starship Construction Complex).
My updates are far from complete, but if there is indeed a problem with the official game files like this, then i'm willing to release it early, so i've attached my updated game files to this post.
To install it, you must do the following things:
1) Open up you Supremacy/Resources folder, then find you Data, Strings, and Tables folders. DELETE all three folders and their contents. This will help to prevent conflictions later on. Do NOT create new folders to replace them.
2) Download the attached file and use the Winzip wizard to unzip the contents directly into your Resources folder (Don't put them into the main Supremacy folder, it must go into the Resources folder). The three folders you just deleted will be replaced and filled with my updated files, which is why I said not to manually create your on folders earlier.
3) Play the game as normal. Do NOT load up any saved files that you have though - in fact, it is best if you delete these. Playing old saved files may result in incompatibilities and wierd glitches. Also, do not allow the game to perform an "update" unless you know for sure there is one available (We'll post about this on the forums when there is one); the game will identify your new files as being "outdated" because they are different to those held on the update servers. It will therefore attempt to overwrite my update with the original game files. As i've said before, You can turn off the auto-updater in the game options menu. Just turn this option off when you want to re-enable the updater again when you know a full update is available.
_________________"Anyone without a sense of humour is truly at the mercy of the rest of us."