I had this problem and I managed to solve it, so I want to share the solution here for future reference.
Solution: Use Calibre 64-bit version.
I see that when I use Calibre 32-bit (which is the portable verison), I got the error "Memory Error" when Memory hits about (if I remember correctly) 2GB - Task Manager showed that my Memory hits about 50% at that time - so I know that it's limitation of the 32-bit verison, not the limitation of my RAM. So I switch to Calibre 64-bit (which required installing) and it won't have that Memory Error anymore.
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