Thanks for the replies.
I have broken the line into smaller sections as recommended, and am able to generate the iso's.
I guess it would help if more information was given when errors are encountered, so you know where
to start looking.
Gone through the PCF, I can see weld display has been assigned in this case. Could you switch-off the weld display in project properties, and connect all the lines again. You should ensure no weld display in the pipe line in 3d. You will get now. I find problem like this only when I draw line with weld display.