unable to perform Remote upgrade using the megafunction

I am using the remote upgrade megafunction in my design in CycloneIII and user-logic is used access as well as to perform reconfiguration.I can write and read to verify the values of osc_int, watchdog enable, watchdog counter. I can even write to the bootaddress register in the megafunction. Since my card actually inputs data/address with reference to 41MHz clock, i am using a 25MHz clock for the megafunction due to its freq limitation. Sometimes , i am able to reconfigure from factory location(bootaddress 000000) but many a times this also fails. I attributed this behaviour to the different clocks used . So i took the input into one register using 41Mhz clock and copied it into another register using 25Mhz clock.This also didnt work for me. MY .jic file programmed into the flash contains two sof files with addresses as 000000 and 080000. If i give the bootaddress as 080000 , the reconfigures never happens. am i providing wrong address. since i am able to read and write through the MF , i guess using two clocks isnt the problem as the reconfiguration happens independently. I am able to send the reconfig signal also, settings are fine yet i m unable to reconfigure.