This issue occurs when you have multiple Spartan-6 FPGA devices in SPI Daisy Chain configuration mode with DONE pins tied together.
While doing SPI Indirect Programming, iMPACT fails programming because the Slave FPGA drives DONE signals LOW (as expected) while the Master is configured with the CORE file from iMPACT to begin the SPI indirect programming.
The workaround consists in configuring the Slave FPGA first, so that DONE is released when iMPACT configures the Master FPGA.
The other workaround is to add a hardware switch to isolate master FPGA's DONE pin for indirect programming only.