1 - I would of course check with another USB blaster just to make sure your Blaster doesn't have some issue.
2 - If you have an oscilloscope at your disposal you should take a look at the JTAG signals on the board just so you can understand what's going on.
3 - If the USB-Blaster is working properly my first suspicion is that you are right on a timing edge that the USB-Blaster is unable to resolve. Here are some things you could try:
a - Try adding some capacitance to the JTAG traces while you try to scan the chain. Like holding a screwdriver tip on the clock line or data line. Sometimes this added drag on the signal can be enough to push things into a working condition.
b - Add a small series resistor into the TDO trace, TCK trace, or TDI trace.
c - Try adding a bit of cable between the USB Blaster and the JTAG header on your board.
Can you describe your JTAG topology?
Jake