The above is not true I'm afraid.

When the onboard flash is set to act as Controller (not Master), the shutter is open before the onboard flash fires (as Controller) to trigger the off-camera flash, so it will contribute a small amount of light to the scene.

This can be easily proved by firing off a shot into a mirror, you'll see the onboard flash in the resulting image.

A simple solution has already been noted by Don, move further away from your subject. Alternatively as has already been stated, radio triggers are necessary to completely eliminate the onboard flash.

I think you need to get out more Dave

Now 13:03 (12:03 in UK) and about the time when Mr. Jones will be kicking somebody's butt coz his shiny new web site isn't yet online.

They must be having technical difficulties, 0Hrs 0Mins 0Secs showing at the moment.
Obviously this bit isn't working

A new replacement camera will probably still have the original firmware version 1.00. It's worth updating it before you send/take it back to the supplier.

Then you need to update it.

My K5-II is on FW Version 1.03 and I had some lockups two weeks ago shooting stock cars. I replaced the battery and had no more issues.

After I got home I noticed that the battery that I had removed was a third party battery, not original Pentax. All batteries were fully charged prior to the meeting too.

Unfortunately it's a fact of life that sophisticated electronic items can and do fail, no matter what name is on the front of it. Sony, Canon, Nikon etc. all suffer failures similar to yours. You were just unlucky but as the camera is still well within its warranty period all should be well in the end and I/we hope that it doesn't put you off from continuing to use your newly repaired or replacement camera.

Have you updated the firmware?

As Ken says, the Hot Shoe Grip can be easily hacked such that modern P-TTL flashes work fine. I regularly use a K5 + Hot shoe Grip + AF540FGZ + Hot shoe adapter F + Synch cord F 5P with no issues, apart from the weight.

It's about the same as using your AF400T, but much better.