Ok, after some research I found the root of the problem.
As it turns out it is not enough to change only FLASH origin address to 0x08000000 in mem.ldl, as it was written in chapter 4.2.2. Since STM32F4 uses core coupled memory, I changed ORIGIN and LENGTH of FLASH, RAM and CCMRAM to correct values and everything works fine now.
RAM (xrw) : ORIGIN = 0x20000000, LENGTH = 128K
CCMRAM (xrw) : ORIGIN = 0x10000000, LENGTH = 64K
FLASH (rx) : ORIGIN = 0x08000000, LENGTH = 1024K
It might be good idea to add in the future Read Carefully paragraph about this issue in chapter 4.2.2.