Hello ,
For the clock speed , in your application code , when you configure the clock to 60M,
after it jump to the APP, it will run these code to configure the clock to 60M, so i think
this not the reason.
While in the bootloader , the clock mode is PEE mode ,before jump to APP, you must
be configure it to FEI mode , or when jump to APP, it can not conifgure the clock.
For the at the start , the clock run from the FEI mode .
Please have a try.
Hope it helps
Alice