I've tried that patch to main.cpp you suggested. Here the output from minerd:
DBG: found zeroes in hash:
7e242ac3d2f4298e502efd7e4b3677cc287114488e1c77c4a1406cba00000000
HashMeter(0): 7994345 hashes, 1587.98 khash/sec
PROOF OF WORK FOUND? submitting...
PROOF OF WORK RESULT: false (booooo)
The output from patched bitcoind is this:
proof-of-work check FAILED...
hash: 9c581ce97e417b9ea6ffb2502041a46ad740a74567e55bbd636d8944cc552995
target: 0000000045120800000000000000000000000000000000000000000000000000
FYI, I'm using bitcoin on a amd64 Debian unstable machine. Both bitcoind and minerd were compiled natively for amd64.
I'll try other algos now, to see if this behaviour is independent of the selected algorithm or not.