On some mainboards the flash IC's Vcc pin is connected to the internal power-rail, powering the entire board if the flash IC is powered externally. Likely it powers other chips which access the flash IC, preventing the external programmer from reading/writing the chip. It also violates the components' power sequence, bringing the ICs into an undefined state.
Please have a look at the mainboard specific documentation for details.
On those boards it's recommended to use a programmer without supplying power externally.
The key to read and write the flash IC is to put the machine into S3 sleep- state or S5 sleep-state maybe with Wake-On-LAN enabled. Another option that sometimes works is to keep the device in reset. This method requires knowledge of the board schematics and might require hardware modifications. Use a multimeter to make sure the flash IC is powered in those sleep states.