Just so you know, most commercial low-sloped roofs that have a manufacturer's warranty on it require quarterly or annual inspections depending on the manufacturer. These inspections can be done in-house, so it doesn't mean it has to be done by a roofer or consultant. Of course, the purpose of the inspection is for someone with roof knowledge to look at the roof so it can be maintained; I do a lot of that as part of my job.
Now, if the contractor did not prime the metal or scuff it (assuming it was pre-finished), then the flashings are not going to stick very well.
Wouldn't mind seeing photos.
You may want to check into Bligh Pacific Roofing, I know they are in your area, but I don't know if they do any residential work. They did repair work for me in Santa Fe Springs, but to be honest all I saw was a bunch of digital photographs when the work was done. Still, based on the photos it appeared they do good work. If they don't do residential, maybe they can point you in the right direction.
And just remember, the redundancy of a built-up roof system provides you protection that can not be offered by a single-ply. When water gets by the first ply on a built-up roof, the mod. bit. cap sheet, then you still have the built-up membrane protecting your building. However, when water gets by the first ply of a single-ply roof, there is nothing else to stop the water from leaking in to your building. If you maintain the built-up roof it should last you 20+ years, and you can repair any blisters, entrapped water, etc. that you find.
What is the difference between APP and SBS? Those are the two polymers generally used to modify asphalt and make it more elastic. Basically, but not always, SBS membranes are mopped down in hot asphalt and APP membranes are torched-down with propane torches. Most likely you have an SBS mod. bit. already, which means it has likely lost 40% of its granule-surfacing if it is 10+ years old. You also probably notice end laps that have shrunk, and your separation along the perimeter edge may also be from where the membrane flashing was mopped down. APP's being torch-applied get heat-fused to the substrate, they weather much better than SBS's, and they don't shrink as much (all roofing membranes shrink).
One more thing. You may want to check into installing insulation with your new roof. The stimulus provides for up to $1500 dollar-for-dollar in some cases, though I don't know if it would apply to you. Certainly something worth looking into though, as it would help reduce any A/C or heating bills you may have. I know, I know, you live in SoCal, but certainly you run the heat or A/C some time.