Here's my latest fault for my 2005 Stilo 1.6 Xbox edition.

I currently have a problem with my fuse box next to the battery, this means if you move the fuse box around the full beams flash on and off.

The other problem I also get is that the engine can sometimes still be running even with the key out of the ignition.

Below is a video I recorded on my phone which shows the engine still running without the key in the ignition.

The only reason the clock is flashing at 12:01AM is because this happened last night and my lights stayed on. I disconnected the battery overnight so it didn't drain the battery.

Nice to see a video of the fun and games!
I'd go straight for the D4 connector as that's the one that usually causes the communications problem. Have a look in the Stilo Guides for how to find it and what to do with it

I dropped it off to the Fiat garage yesterday, I called them up today and low and behold they found no problem, even though I know for a fact there IS a problem.

I called my breakdown (GreenFlag) and they sent out a tow truck, he diagnosed that the problem WAS the fuse box and that he wouldn't touch it because if he did then Fiat wouldn't want to know.

I have told the Fiat garage specifically to move the fuse box around and they quite clearly didn't so it's still at the garage now.

They should be back to me later today and if they still don't find the (obvious) problem then I just want the car back and I'll send it somewhere else.

Did you show them the video?
You have a permanent engine fault light lit on the dashboard so of course there is a problem. I'd take it somewhere else where there might be a bit of common sense

(Mind you, I'd probably sort that D4 connector myself)

It must be the D4 connector, I remember seeing it not connected to anything the other day, actually it's not been connected for a while, ever since I had the previous problem where my ECU got spiked. The same garage must of disconnected it and not connected it back again.

Do you know if it's vital to the car if it's connected and specifically what does it do?

EDIT: Also I rung up the garage again to see was status the car was and they said the car was ready so they still quite clearly haven't found the problem even though I told them how to get to it.

I'm just gonna get the car back because I need it to travel and I'll follow the D4 guide to fix it myself.

There's a few connectors under the fusebox, some are connected and some aren't as they're for other options not fitted on your car. Anything that's not connected leave alone

You won't have gotten anywhere without the D4 connector connected. Look in the Stilo Guides for where it is, what it looks like etc.