I'd check the ref voltage to the USB II connector first and any board jumpers for the JTAG chain.
Then if that all looks good, reduce the TCK frequency in chipscope/impact to a low setting (e.g. 100Khz) to see if that makes the connection reliable. If so, you have a signal integrity issue on the JTAG Chain (quite common).
Digital Design Golden Rule: If its not tested - its broken.