Solved :
It was hard disk issue , bad sectors and couldn't read files correctly .
since reset to factory defaults makes the new data applied to ram directly .. it's OK .
but after reboot and load settings from Disk .. Nothing is OK .
I noticed it won't read queue statistics in webgui says I have to set traffic shaper while it's already set .
and even after resetting to factory defaults , some rules doesn't work as expected after setting them up.
also by many reboots I noticed there is a fast warning messages about mounting disk in pfsense boot screen .
now everything works fine after replacing the disk .
Thanks anyway :) .