@derdigge1982, Thanks for the tip. Unfortunately, because this new motherboard I thought would save me appeared to be not that good (see
https://bitcointalk.org/index.php?topic=3027617.0) I had to switch back to using that motherboard that gave me some troubles. This machine happens to be not only a 6 GPU rig but is also my VM server I use for work. One of wich VM is my actual TFTP server! So there's no way I can boot my host system on a TFTP servers that is hosted on this very same host

... D'oh!
Having said that, If I can't find any other solution I'll check if my router can do that.
@konqueror, yes I tried as root and that doesn't help (but I admit I quickly edited the pasted command line :p)
@theodrim, what I understand starting atiflash with strace is that it scans the whole /sys/bus/pci/devices/ entries looking for the "config" pseudo file. whenever one is found it reads few bytes from the file using pread64().
When done, it gets the status of a file and mmap some memory and then print the "no adapter found" message:
open("/sys/bus/pci/devices/0000:80:03.0/config", O_RDONLY) = 3
pread64(3, "\4\6", 2, 10) = 2
close(3) = 0
...
fstat(1, {st_mode=S_IFCHR|0620, st_rdev=makedev(136, 0), ...}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f1c86c52000
write(1, "Adapter not found\n", 18) = 18