When you update the bios to v1.4 using the latest flash utility, it will show "Erasing Done and then Programming Done". But actually the process has not been finished yet, you will need to wait about 30 seconds and then the message of "Flash Complete..." is showing up, this will complete the flash process. 

By doing this, end user will assume when it display "Programming Done" message, it has complete the flash process which is wrong. We need to wait until the "Flash Complete..." message has displayed on the screen in order for completing the flash process. 

By any chance we can remove the message of "Programming Done" and only prompt for "Flash Complete..." so customer will not turn off the system or reboot the system when they see "Programming Done" message pop on the screen?

The new version ADSFI708.EXE has fixed this issue. When you finish the BIOS , it will show the "Verifying the ROM data now" message before it showed up the "Flash Complete".

Here's what I understand about PAT. 

As you may or may not know adding pipline stages to any execution unit will allow you to run it at a higher frequency but it will increase the latancy from start to end (measured in clock pulses). 

Now, in order to ensure reliable operation at 800MHz FSB intel added 2 pipline stages to the memory controller (as based on the original dual memory controller in the E7205 chipset) 
This they called i865PE and it will only put into action these 2 stages when 800MHz FSB is applied (which it needs the bios to tell it is the case) 

Intel take the better yealdes of 865PE and validate them for 800MHz with the 2 extra stages disabled. 
These they call 875P. 
A 875P bios with PAT enabled simply does not "tell" the chipset it it running at 800MHz so the extra stages are inactive thus reducing latancy relative to a situation where these stages were activated. 

A hacked 865PE bios will simply follow the 875P bios rule of not notifing the chipset it is running at 800MHz. 

PAT is not an optimization, it's a de-un-optimization