> Thanks Marc,
> No, the *only* difference between being able to program the fpga with 
> 'progdev' is whether or not I'm running tcpborphserver2 from the 
> command-line, or whether it is running from when the board booted up.  
> It makes no difference what bof I use.

Odd, really odd. 

A running process has lots of information in /proc/<pid>/

In particular maybe could you check that 

/proc/<pid>/cwd points at the same location 
/proc/<pid>/exe is really the same binary
/proc/<pid>/cmdline is the same commandline

and (bit more effort) that

/proc/<pid>/maps loads the same libraries 
/proc/<pid>/fd   has similar file descriptors open
cat /proc/self/environ | tr -s '\0' '\n' shows no unusual environment variables

regards

marc

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