Flash Programmer Stalls

When I go to program the flash on my system. It prints out:

# Creating .flash file for the FPGA configuration

"$SOPC_KIT_NIOS2/bin/sof2flash" --epcs --input="C:/Development/XXX.sof" --output="XXX.flash"

Then it sits for about 2 minutes before it proceeds to actually flash the FPGA. When I check the processor usage, there is little to no activity. The strange thing is that it used to go very quickly, it would run the java script to convert to the .flash file in a few seconds. Now it just hangs for a very annoying amount of time. I have checked to make sure that my java is up to date. I just can't figure out why it just sits there before proceeding. I would appreciate any help.