I learnt that the address space (0x60000000 to 0x6001FFFF) which I was using was overlapping with the IPS address space. Now I have changed my address space to 0x90000000 to 0x9003FFFF. And I think I'm getting proper addresses on my logic analyzer. There are minor glitches though between address and data changes on the 16 bit data lines.
PS. The default address space in MCF52259 is:
Internal 512 KByte Flash: 0x00000000 to 0x0007FFFF
Internal 64 KByte SRAM: 0x20000000 to 0x2000FFFF
1 GByte Internal Peripheral System Address Space: 0x40000000 to 0x7FFFFFFF
Ameet Kaustav.