I changed the injection rate from .5ul per min to 5ul per min. Recovery has been much, much better for past two weeks. Got my idea about changing rate from Restek web site. OK on another identical system. If main sample is an Aroclor, such as 1254, that Aroclor is recovered fine.
Cleanup procedure leaves sample in hexane.
Injection volume is 2 microliters with a 1 microliter chaser. Main sample concentration is .25ppm. Perhaps, there is some contamination inside of of one of them that is causing your problems. If you are using deactivated liners, maybe they are no longer deactivated. Those are just some thoughts off the top of my head.