Thanks for the help Yuri!
Although our chip is 1.3 version and there is not heavy load since being in boot process, the problem seems to be related with internal DMA. For example, if simple internal DMA is used Multiple block read cannot be realized; additionally if ADMA1-2 is chosen then even Single block read cannot be done. In these situations, the Present State register shows me that SDOFF is set, in other words SD Clock is gated off.
I tried to re-assign SDCLKFS and DVS fields of System Control register however couldn't restart the clock. What is the procedure to do this?
Also I tried to use external DMA for the transfer from internal buffer to the system. I disabled internal DMA and enabled external DMA from Vendor Specific Register. But internal buffer is again over and transfer cannot be finished succesfully again.