Atmel START: Custom Board project not working on SAM E54 Xplained Pro board

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I want to develop an application for the SAME54P20A. I will create custom PCB for the project, that is why I don't want to use the SAM E54 Xplained Pro template in Atmel START. I just want to select the SAME54P20A as target and go from there. However, when I do that to project just does not run. It compiles fine, it uploads fine (to the Xplained Pro board) but it doesn't run, cannot get to a breakpoint in main(). When I manually pause execution it gets me to the Disassembly tab and it's stuck on "F3AF4804 ??? memory out of bounds or read error".

 

When I run Example projects for the board then everything works just fine!

 

I attached some screenshots from Atmel START and the project folder 7z file!

 

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