Okay, this happened to me also, what happens is that when you add a goalkeeper or third kit with creation centre, it is adding the kits in the zdata_1.big file, when this file gets too big, Kit Raptor has problems finding the files to add the 2GK kits.
Although I have reports of people working with a zdata1.big file of over 60 Mb, usual critical mass for this to happen is around to 40MB. When this happens your game will begin to behave erraticaly, sometimes crashing for no apparant reason.
What you need to do is this :
1) Take a full backup of your data folder and store the files in a safe place.
2) Open Creation Centre, and note the Team_ID's of the teams where you have third kits and/or goalkeeper kits failing.
3) Create a new folder on your c: disk and name it for example "kits transfer"
4) Open your zdata1.big file with BIGGUI tool and look for the files like this :
playerkittexobj.texobj463104248046875__texture23_2_0_xxx.fsh
playerkittexobj.texobj463104248046875__texture23_3_0_xxx.fsh
where the xxx is the Team_ID you noted in creation centre of the teams where the kits are not working.
The first is the goalkeeper kit and the second is the third kit.
Now select these files and export them to your newly created folder "kits transfer" (the second blue arrow pointing button in BIGGUI), then delete the selected files with the red cross button in BIGGUI. Finaly rebuild (the blue R button in BIGGUI) your zdata1.big file. Then close BIGGUI.
5) Open zdata7.big with BIGGUI and click on the import button (the blue arrow pointing inwards) then browse to your "kit transfer folder" and select your exported .fsh files 3 AT A TIME (not more or it will crash!!), hence and repeat.
Once all files are imported reselect them in the list in BIGGUI, then compress them with the appropriate button in BIGGUI. Finaly Rebuild your Zdata7.big file.
6) Rebuild your fat file with your favorite FATBUILDER program (I recommend FATGUI version 1.3 for best results though)
7) Re-import your failing kits with Kitraptor
8) Rebuild your Fat and Bh files again like in step 6.
9) Launch Fifa and enjoy your kits!
Notes :
If something goes wrong, restore your saved data folder and restart from the beginning.
I used zdata7.big here since it is the best suited for kit files (until it grows too big too and then take zdata10.big)
You can also gain additional space by moving the cc imported player face files from zdata1.big to zdata15.big
Do NEVER under any circomstance touch zdata2.big, zdata4.big, zdata17.big and zdata18.big as these contain essential data and do not support additional files cohabiting inside the big, you have been warned.
Also be careful with zdata16.big which contains stadium and balls data and is often edited in patches like turf patches and such, if your game crashes for no reason this is the first file to look at, if you find more than one uncompressed file with BIGGUI inside, don't bother trying to fix it, it's time for your last restore...
Also, if FATGUI gives you error messages it means you got more than one copy of the same fsh file in different zdata.bigs, this can make your game crash or eat a lot more memory than is necessary to run the game, take note of the filenames and go look for them with BIGGUI, delete one of the two (or more) recursing files.
Hope this helped.