I had a similar issue with 2 pairs of FWSMs. One pair would discover fine, but the other pair (on same firmware) would seem to discover but then I would receive the "no devices found" message.
I logged a case with support. They came back with this message:
"Thanks for you patience. I received an update from our dev team and in their testing they found that this is a bug with the discovery engine which will be resolved in the next release. The only work around is to add the devices manually through the ADD nodes feature and not the discovery."
Thank you, that works perfectly. We have only just got NPM and have so many devices to import I hadn't considered doing anything other than using discovery.