I have a Gateway M320 laptop which I recently replaced the motherboard on due to bad USB ports.
The laptop is reassembled, but now all I get is a flashing power light. There seems to be no control of the power button. The power comes on as soon as it is plugged in, (no need to push power button).
The fan is working normally, I have reseated the memory and hard drive and have gone as far as replacing the processor, all with no results.

Any assistance will be appreciated.

Some laptops have a power on switch which is activated when the machine is opened, others have a seperate switch for that function, some may have both.
Off hand I'd say that there is an alignment problem with your switch that probably occured when you replaced the cover, etc., either that or the switch itself is defective.

I removed and reseated the motherboard, processor, memory, hard drive. The laptop boots and runs fine.
The only problem I have encountered is that it powers up as soon as the power cord/adapter is plugged in and the laptop will not keep time., which I suspect is a battery issue.
As for the power up problem, I have no clue.

I think you should replace battery, or use just adapter.