JTAG Connector and pull/downs are okay
M25P40 DATA0 needs the 25Ohm as mentioned in C3 PDF.
If your byteblaster handles the pcb correctly and the usb blaster does not, then 2 possibile reasons can be.
1. check your usb blaster, try to change the yellow flat cable to a normal ribbon type (like your harddisk cable inside your pc) and make this cable as short as possible (5cm) some usb blaster Rev.b we hav had these problems
2. check your pcb for trace length, i remember a pdf teling max trace length for the jtag signals. again make these traces as short as possible
what messages do you get when starting jtagconfig.exe ?
how is your layerstackup ?
be aware of the 3,3V theme about Cyclone III devices, we moved to 3,0V because of that.