It's all about the process of elimination with leaks. I had 3 in my ute & it was driving me insane trying to find the source & eliminating it
http://forums.justcommodores.com.au/vy-holden-commodore-2002-2004/250639-drivers-side-leak.html. My advice to anyone experiencing leaks is to do the following:
Take off the door card(s) & check the plastic weather shield for tears & non sealing sealant. To check, hose down your door & watch where the water accumulates. Check the drainage holes under the door.
Check all door rubbers to see if it seals properly. Door rubber components cost $80 each new from Holden. Again get someone to hose the affected area.
On the body check the rubber plugs. They can perish over time. cheap to replace. Stick your fingers inside to feel for any water.
Take the wiper arms off & the plastic shroud(s). Look for signs of accumulated water. Clear any leaves & clear the drainage holes. Check the seams on the bodywork & the rubber & sealants around the window. Again use a hose to check. If the glass needs replacing, do not use O'Briens but a better established company to replace the glass. Check rubbers around the glass.
If required take the kick panel off & feel for dampness or water. You may also need to take the plastic trim around the door frame off to find the leak. Don't be afraid to pull up the carpet & check the seams & any rubbers on the floor for signs it may have perished. Look at the carpet for mould patches. Remember water goes down & not up.
Check the B pillars as water can accumulate inside.
If water is in the boot, check the pinchweld rubber. look for water trails (and rust). Check carpets, spare wheel well, seams and any previous repair work.
Water leaks are a pain in the backside so instead of getting frustrated, think logically & eventually you'll find the source of your problems. Also do a search here as others like myself have had these problems.