I've not had WorldEdit work with mod-added blocks (specifically, the mods in Feed the Beast/Mindcrack 8.1.1) in the last twenty or so BukkitForge builds (and half-dozen or so WorldEdit builds) I've tried. Region selection works fine, movement commands (e.g., /ascend) work fine, region modification commands (e.g., /expand) work fine, but any non-vanilla block ID produces "block name '_number_' not recognized." Region clipboard operations also fail to manipulate any non-vanilla block IDs, which can make accidental pastes impossible to //undo without manual repairs.
Basically, WorldEdit 5.50 release and snapshot builds only seem to work on vanilla blocks. Which, on a modded-Forge server, makes WE pretty much useless.