help wrt flash photography in manual mode

So I've just bought a flash (Metz 52) for my Canon 60D and I don't quite get the expected results in manual mode (the camera that is, flash is always in ETTL mode, not manual, Ev at 0), sometimes the foreground is overexposed, sometimes it's underexposed.

Since the ISO is 'stuck' at 400 when the flash is active, setting first the aperture to get the desired DOF (say f/8), then I start adjusting the shutter speed to get the exposure indicator right in the middle of the scale

The problem is if there's not much ambient light and the lens doesn't have IS, I would end up with say a shutter speed of 1/20s which would 'catch' my hands' shaking.

One thing I noticed is for the same foreground & background, same ambient light, the aperture and shutter settings would be the same at ISO 400 and centered exposure regardless of whether the flash is active (turned on) or not. Logically I would think the camera should know the flash will output some light so having the same aperture, shutter and ISO would mean the exposure should go 'over' when the flash is active vs. when it's not.

On top of this, when I can't keep the slow suggested shutter (for centered exposure) and have to raise it to say 1/100s, the exposure will go as much as the left edge of the scale but if I still take the picture it is many times more or less well exposed due to the extra light the flash output but I can't trust the exposure indicator anymore, I could be at -3.5 or at -13.5 for all I know (since both values are out of the scale).

What am I missing here?

And one more thing: in Av mode, the camera has 3 settings wrt to flash sync:

1. auto

2.sync of either 1/60s or 1/250s (calculated by the camera)

3.1/250s fixed

I understand what 2. and 3. do, however I don't know what sync value gets set in 1. if my shutter speed is outside (slower or faster) of the 1/60s to 1/250s interval.