I am having trouble flashing a partial bitstream on a Spartan 3A starter kit with iMPACT.

I made a simple counter design, and used FPGA Editor to modify a single lookup table.  Both designs work fine on their own.  I synthesized and implemented each design in ISE and generated the bitstreams following XAPP290 and AR #18416:

bitgen -g Persist:Yes -g security:none top.ncd

bitgen -g Persist:Yes -g ActiveReconfig:Yes -r top.bit top_altered.ncd top_par.bit

There are no errors, except a warning about using the "Persist" option without a CONFIG_MODE constraint.  And when I flash the initial bitstream, it works fine.   However, when I flash the partial one I get a CRC error and a "Programming Failed" notice.  In addition, the design stops working and all the LED lights become half-lit, as if they are flickering back and forth.

Has anyone tried anything similar?  I've shuffled around a few bitgen options, and even disabled CRC, but nothing seems to work.