By some remarkable coincidence I opened this as I got of the phone too someone 
having very problems on a a different board which had worked fine a couple of 
weeks ago.

On Saturday 10 April 2010 05:06:39 Wookey wrote:
<snip>
> And how come the CPLD boards work when chained but not stand-alone?
<snip>

Hooking them into a chain redrives or modifies the signals.

This sounds very much like a signal integrity issue. If the scan chains are 
wrong then look at what the all the lines are doing. Don't forget to check 
the reset line too.

-- Charles