Problem with new install of 9.1 with Cyclone III

I'm setting up a new PC and migrating my existing Cyclone III design to it.

The design has worked without issue over many EPCS loads/ FPGA configurations using the old PC.

When I move the design to the new PC everything seems to work ok. I can download the design sof and the FPGA works fine.

On the new PC, If I run the NIOS II flash programmer to convert and download the sof and elf no errors are reported.

The problem is if I cycle the power on my PCB the FPGA doesn't configure. I know the elf was downloaded correctly because if I use the Quartus II programmer to load the sof I can see that the code was updated.

Form the old machine I have no problem with the same version of the design. The machines are identical software-wise as far as I know.

PC 1) old, slow and works; Windows XP, SP3 32-bit, single core Xeon processor

PC 2) new, fast, FPGA configuration from EPCS fails: Windows XP, SP3 32-bit, quad core Xeon processor

Both machines are running Quartus II 9.1 SP1, NIOS II EDS 9.1 sp1 (using the software build tools for eclipse)

I tried with both USB Blaster Rev B and Rev C and get the same results.

I don't suspect a hardware issue since the hardware has worked consistently for over 6 months and still does running from the old PC.

On the other hand I can't find any differences in the software setup either.

Any ideas on what the problem is? Any things to look at to debug?

thanks