Chekc that you're not trying to replace a bitfile which is either write protected or you simply don't have the rights to create a new file in that directory.
IIRC the old bitfile is deleted relatively early int he compilation process but the generation of a new bitfile is attempted only after the full compilation has completed. Anything which will prevent you from creating this file will possibly lead tot his error.
I'm pretty sure I ran into this problem before and I solved it by changing the permissions on the folder I was trying to create the new bitfile in.