about component made by user logic

Nope that's fine, so my next question is did you create a HAL driver for it or are you simply reading and writing using pointers?

If you are using pointers make sure you declare them as volatile to make sure they are not being synthesized away at compile time. Also put your compiler into debug mode with -O0 optimization just to make sure it's not simply the compiler causing this. If your code is not too big you may also want to use the debugger to step through your code where you perform reads/writes to this custom peripheral to find out when it actually breaks (could be that it's fine and a bug somewhere else is the cause).

Cheers.