A general question about peripherie ????

I have two programs one for bootloader and one for application program.
And i also disable all the interrupts before i jump from bootloader to application program.
When i initialise a peripherie part (i.e. lcd) of the application program in the bootloader and make a jump to application program,
then the peripherie part is goes into an endless while loop. The reason why is this happening is that, the pheripherie read a register values not correctly.
By the way the peripherie part initiated again.

But when i initialise the peripherie part only in the application program and do the same procedure above then everything works fine.

Can someone explain me why is that happen and how can i solve this problem?
Do i have to execute a reset after before application program start? (maybe this can solve my problem)

Thx