Are you saying the portraits for Bastila, and Carth within KSE are wrong or are their portraits within the game wrong? Do you have portraits.2da in the override?
Since you mentioned that you upgraded from 2.0.7 when this occurred, you might have leftover files in your temporary directory causing problems. Browse to c:\documents and settings\(your username)\local settings\temp and delete all folders that begin with "pdk". Then try making portrait changes with KSE again and see if it starts appearing correctly.
If that fails, make a kse.log file in the same folder as KSE and try doing the modifications again. The kse.log file will capture extra information for debugging. You can email it to me at the email address in the kse-readme.txt.