No solder paste was applied on Thermal Pad for AGND. What would this do?

I can only suggest that you have some of your failures re-worked so that you know the device is down correctly. That way you can (pretty much) rule it out when it comes to troubleshooting failing boards.

Can you monitor the voltage from the device during the boot process? Hook it up to an oscilloscope. Make sure you try this with 'cold' (room temperature) boards so there is no residual heat involved - i.e. give it the best chance it will get. If you can detect a drop in the voltage during boot then you may be onto something. If not, and it is regulating correctly throughout, then even though the device is not down correctly it will be doing what's required of it.

Cheers,

Alex