if i run a new section of pipe or place new fittings on a model connected to a line which has custom data fields filled out, they do not pick up the custom data from connecting line/fitting. Is there a setting somewhere which allows this to happen.

You will need to monitor and modify after the change. You can use a tool like MTOWorx to easily filter and find the missing data.

If the data is the same for all parts, you could also set default values in the SpecView palette.

The easiest way is to select all components in pipe and go with GCEDIT to change custom data for all. We also find out that custom data field is tricky and not reliably.