Code:
Lastly, in the version I'm testing, I tried the tests with factoring depths
 of 48 and 49. I got B1 and B2 bounds of 40,000/50,000 and 430,000/575,000 
respectively. However the amount taken to complete these tests with such 
different bounds weer almost the same. Does this have to do with zero-padded 
FFTs? Or is there something wrong with this picture? Here is the relevent log
snippet:
George,
Do not worry about my second question. I was not able to replicate it! I do not know why it happened the first time but it doesn't seem to be happening now! With lower bounds the program does indeed take less time.

Finally, I checked the linux version with some know factors, stage 1 and stage 2 and they were all found. Pity I haven't found any new factors yet