Frustrating, isn't it?
You are far from the only person to find that the AF360FGZ underexposes pretty badly -- frequently, routinely, but not always repeatably.
p-ttl underexpose - Google Search
Not just the 360, but other Pentax P-TTL-compatible flashes too.
Many workarounds have been proposed (e.g., using "Auto" mode as you noted, or linking the autofocus point to the metering point, or dialing in some compensation manually), but none of them is really a solution.
Personally, I have found that the flash works pretty well with my FA 50 f/1.4 lens, and I get decent exposures, but with the kit 18-55mm lens I usually get significantly underexposed shots. But not always, so I can't just dial in a positive flash exposure compensation value and leave it there, or I'll get some overexposed shots.
Argh.