It was working fine but the battery is not good so sometimes it just turned off when the car ignition was off before I could actually switched the TT off.
It is a TT XL IQ routes version
Navcore 9.5.10
Bootloader S5.5277

It stops at the startup screen.

If I connect and control it from TT Home then it asks for the country, and some basic settings such as miles or KM and the time and after that it will work fine but only when controlled via TT Home. If I have maps on there then they will work or if there are no maps then it will go as far as telling me there are no maps.
A normal reboot and it still stops at the startup screen when not controlled by TT Home.

If I reconnect it to TT Home again then it will ask again for the country and the basic settings so it seems like they are not being stored.

What I have tried:
1/ Reset by holding the power off switch down.
2/ Full format of TT, installed the Navcore 9.5.10 without using TT Home.
3/ Full format of TT, installed Navcore 9.5.10 via TT Home.
4/ Also used the clear flash tool.

I have done the above things in many different ways but I have never got it to go passed the startup screen.

Does anyone have any ideas what I can try next.
I thought about reinstalling this bootloader thing but I can't seem to find out how to do it so that may not even be possible.

Any ideas?

Still no answer on your question.
As far as I know you've done already everything to fix your problem.
But you've re-installed Navcore 9.510, did you the next test with or without a map ?
Normaly without a map you must get "no map found"
When you've doubts about you Bootloader follow the next steps
Get Bootloader 0.0001, install this version first, ti will make you possible to install any other Bootlaoder you like.
Be realy carefull with this update, don't interrupt the process, also with the next updates to the Bootloader you want.
If possible full charge you battery firts and connect als to a powersupply.