I just figure out the issue.
It turns out that since I had installed kinetis Studio on my computer
and opened my workspace that I have been using with CW 10.5 and CW 10.6 along with PE 10.4 suite,
Kinetis Studio change the PE preferences to use the PE from SDK.
So, when I went back to open the same workspace on CW 10.6 the scripts from SDK are not compatible with scripts on PE 10.4 Suite.
This is what was causing the issue.
So I let CW 10.6 to use default preferences for PE and that fixed my issue.
I hope this can help some one else.