EDK oddity

So I have a Memec P7 evaluation board with the EDK and a Parallel 4
download cable.  We are doing something very basic here to just get
our feet wet.

All we are doing is writing to the UART a simple hello world program. 
We wrote some C code, and then stepped through the base system builder
using this board.  We went thru all the steps in the EDK and
downloaded right from the EDK to the board.  Hooked up Hyperterm and
viola- there was hello world.  Hit reset on the board and there it was
again.

So far so good.  Then I figured I would go into the debugger and check
out the SDRAM.  Run XMD- connect to the debugger and write to the
SDRAM.  The values do not stick.  Odd.

So I exit the debugger completely and simply hit the reprogram button
in EDK.  It says it downloaded the bit file but now hello world
doesn't work.  I am simply reprogramming the FPGA here.  It doesn't
work.  I reset the program, the PC, the eval board, everything.  It no
longer works.  I cannot get hello world to work again.  I do a make
clean in EDK (both HW and SW).  Nothing.

So I reprogram the FPGA and connect with the debugger.  Now the
program does not work- but I can write to the SDRAM locations and they
stick.

I repeated this a couple of times.  If I build a system from scratch
it will work.  If I use one after I download and open the debugger- it
does not work.

I attempted to trace the program- but my SW guy is on holiday.  It
craps out on some MTCTR instruction.  Some special purpose register
move thing.

Our FAE is stumped to.  Anyone seen anything like this?  I would
thing- reprogram the bit file into a UART that has been reset- you
should be good.  Apparently, not in this case.

Thanks,
MS