Cooling fan on with ignition
 

I'm pretty sure it's normal for the fan to come on if you turn on the ignition and the engine is warm. It may even do it cold, I'm not sure, but depending on what you were doing before you observed this, it may be normal.
In the normal case it will turn off after a bit of time. Like 20-30 seconds. If it doesn't, and the engine is cold, and the fan just keeps running for minutes, that's weird.

I'm not sure how P0480/P0481 are actually detected by the ECU, but one mechanism may be that it turns on the fans (or thinks it does), but the coolant temperature doesn't go down. On the 8 it may have another mechanism, like some kind of load reading on the circuit, but long story short, the ECU thinks the fan relays are not working. So while you've disconnected the mod, is it possible you need to reconnect the original wiring?

Here is how the cooling fan controls work in an S2 in tabulated form:

https://cimg5.ibsrv.net/gimg/www.rx8...aa03497bbf.png

Per service manual, this is how the P0480 and P0481 work:

https://cimg4.ibsrv.net/gimg/www.rx8...21cc45bb39.png

Naturally, it covers how to repair the codes. It's mostly checking open circuits, shorts, poor connections, etc. ASH8 has the service manuals posted up in this forum.

Thanks Jinx so according to that my fan shouldn't be on at start up ?

Definitely not on a cold start unless you have your A/C on. Hot starts will depend on the ECT, as the table indicates.

Aircon off. I have swapped around relays and the same. The fan that is operating when cold is number 3 in fuse box

https://www.rx8club.com/series-ii-te...manual-247192/

Download the workshop manual and start following their procedures for troubleshooting. I would think there is a short somewhere in the circuit.

Is your coolant temp sensor OK?

Not sure mate going over it now. How can we check ?

I've heard of people wiring up a manual switch somewhere in reach of the driver. Any chance the PO did this?

That would be the fans on low mod. I did it. Works great when the AC is off. If this was done, there would be an extra wire running from the switch to the relay box, and another wire running from the switch to ground.

Who knows? You get those electrical pixies dancing in a circle and all bets are off.

We're you able to correct the issue? I think I have the same issue.