The custom IP logic generated by CIP Wizard is fine. Theproblem is on the driver template; it assigns the same offset value for every register as below:
#define IP_SLV_REG0_OFFSET (IP_USER_SLV_SPACE_OFFSET + 0x00000000)
#define IP_SLV_REG1_OFFSET (IP_USER_SLV_SPACE_OFFSET + 0x00000000)
These values are defined in the "IP_name.h" file.
To resolve the problem, change the "0x00000000" to "0x00000004" for the second register, and "0x00000008" if there is third register, etc.