We replace many of these types of door systems here in Vancouver. I would suspect that your install was never properly done and if you can you should remove it all - clean it up and re-install it. Much of the waterproofing offered by this type of system is in the bead of silicone on the back side of the hardware when it's installed. Over time this can shrink and crack and leave voids in the protection.
We have found that many of these door systems leak when sprayed with water so we replace with better kits - framed or frameless. Before you spend two much time you might consider replacing the whole thing. Often this can be done for less than $500.00 installed.
This last leak we found cost the home owners a small fortune in flooring repairs. The result of a poor door, water running behind the system and a nanny that didn't care.