Hey Munees,
So if you trace from try_init_kernel() (https://github.com/seL4/seL4/blob/master/src/arch/arm/kernel/boot.c#L375), you'll see that on line 375, we do map_kernel_window().
Map_kernel_window() changes the mappings in the kernel's page tables in RAM. But the problem is that the cached TLB mappings in the processor will not be updated to reflect the changes we made, until we invalidate the processor's TLB.
So we later on proceed to invalidate the TLB (https://github.com/seL4/seL4/blob/master/src/arch/arm/kernel/boot.c#L222) by calling activate_global_pd() shortly afterward inside of init_cpu().
Activate_global_pd() is a preprocessor macro which is #defined to just resolve down to activate_kernel_vspace (https://github.com/seL4/seL4/blob/master/src/arch/arm/64/kernel/vspace.c#L461), which is the function in which you are now seeing problems.