I tried to follow the guide on this site here but got no reply. Maybe I posted in the wrong place (and maybe that guide should be merged here). Nevermind.
I solved the problem myself and thought I share it here in case anyone has a similar issue.
Apologies for a long post.
The Problem :
The problem with my motherboard (Z77X-UP5-TH) was that CH341A (attached to the BIOS flash chip via Clip cable) could not provide enough power to the flash chip.
The reason was obvious: when you attach the Clip cable which carries the 3.3v for the flash chip, it will also try to power up EVERYTHING else that is on the 3.3v bus on the motherboard. The result is that the voltage regulator on the CH341A is not capable and the voltage sags to 1.68v. Thus the Flash chip was never detected by the software.
The Solution :
1. Provide an external 3.3v supply on the Clip Cable attached to the CH341A. I simply built a USB 5v-to-3.3v supply using a KIS-3R33S module that I happen to have in my spares (very cheap on eBay). This converter can supply around 1A of current:
2. Cut off PIN 8 (VCC PIN) on the Clip adapter that connects to the CH341A so that 3.3v CANNOT go up the Clip cable. Then solder two wires to the adapter on PIN 4 (GND) and PIN 8 (VCC):
3. Attach the Clip cable to the adapter:
4. Attach the Clip cable + adapter and the external 3.3v supply to the CH341A:
5. Plug both the CH341A and the External USB supply to a working PC.
6. Attached the Clip onto the BIOS Chip.
7. Attach the ATX PSU to the motherboard (with the BIOS chip) BUT DO NOT power on the motherboard via the case power switch (but only at the Mains supply). On my motherboard there’s board power switch with an LED which lights up to indicate ATX PSU is ready.
8. Start the CH341A software of your choice (I tried 1.29, 1.31, 1.34, Flashrom, AsProgrammer, etc) and all will now detect the BIOS chip.
I was then able to read back, erase, write and verify the Main BIOS chip with my BIOS and the also the Backup BIOS chip with Gigabyte’s stock BIOS.
I read-back the BIOS’s with different software versions and types and binary-compared them successfully.
The motherboard is now recused.
A note on the external supply: even though it is rated over 1A @ 3.3v, it does not regulate well. When not loaded, it supplies 3.26v. The voltage drops to around 2.86v when the Clip cable is connected to the motherboard BIOS chip. That voltage is within the tolerance of the BIOS chip. I measured the current drawn from the 5v USB supply it was drawing around 380mA during read/write.
Thanks for the guide. It helped me save this board.