Capture.ini has two locations ,one is in folder :\Cadence\SPB_16.6\tools\capture\
Capture.ini the Second is in :\Cadence\SPB_Data_16.6\cdssetup\OrCAD_Capture\16.6.0\Capture.ini
Compare the two files you can find that the second capture.ini file is more detail than the first one. you can backup the first capture.ini file and then delete it.then open the capture CIS you can find in the session log that the capture CIS use the second Capture.ini automaticlly.
in order to let capture CIS know where my library is and constraint
[Part Library Directories]
Dir0=D:\XXX\
in :\Cadence\SPB_Data_16.6\cdssetup\OrCAD_Capture\16.6.0\Capture.ini before [Application] line
then save the file and restart capture CIS everything works fine.
Good luck!