Dear Dhananjay,
As far as much experience can tell, it is typical fort the simulation to take more time with the sequence having been increased that much, so it cannot necessarily be considered a bug. However, I suggest that you reduce the number of samples per pit if it is possible so as to make less samples all in all that way. You can also improve your hardware (as I did to overcome these problems), or install 64-bit windows if you are currently using 32-bit version and if it is compatible with your software.
Regards