Thanks to all of you for taking the time to go through the files and help me solve this issue. I have figured out what the problem was and have managed to solve the issue. Now EFB v2 is showing the correct airport layout including KLIA2 and RW15/33.
The issue was that the database of EFB v2 was using the incorrect BGL for the WMKK airport. I had 2 versions of WMKK in my addon scenery folder, one was the older version in a folder called KLIA, and the second was the newer version called WMKKv2_2015. After lonewolf47 pointed out that the BGL file i had uploaded only had 2 RWs, i double checked my scenery in FSX and found that the sim was showing all 3 RWs with the KLIA2 terminal. Then I went to the scenery library of FSX to check which directory it was using and found that it was using WMKKv2_2015 folder's WMKK_ADEX_TIC.bgl; reviewing my first post, I saw that EFBv2 was using the BGL from KLIA folder and not from WMKKv2_2015 folder. So I moved the older KLIA folder out of the FSX directory and rebuilt the database for EFBv2, and that solved the problem. Now all is good with the EFBv2 and the WMKK scenery. It is just a little surprising to me that EFBv2 database scan picked up a folder (KLIA folder) that was not even in the scenery.cfg as it wasn't added to FSX scenery library.
Anyway, sorry for the long description to my problem, I hope it helps someone else down the road. If the admins want, you can delete this thread or mark it as closed or however it works. The issue is resolved for me! Thank you all again!