This has happened to me on a few occasions and as a result I've given up on querying Shotgun from inside Nuke on CentOS.
When I query Shotgun from Nuke - for example to check what is the latest version for a specific shot, the first query goes through, but the second crashes Nuke. It happens in Nuke 6.1v1 on CentOS 5.3 64-bit. The Shotgun query is fired when an user presses a custom PyScript button. If I remember correctly, the same thing happens when the query is run from the Nuke Script editor.
It also happened when I tried Frank's ShotGunDropper tool on http://www.nukepedia.com/gizmos/python-scripts/nodegraph/shotgundropper/. In that case, when I drag and drop an URL for a given version the tool works fine. When I drag & drop the same URL one more time, it still works fine and creates another Read node. When I go to another version's page and drag and drop it's URL, Nuke crashes. However, this is not happening when I try it from Nuke 6.1v1 on a Mac mini running OS X 10.6.5. PS: The tool finds the version id doing a pattern match on the URL, then runs a Shotgun query against the version ID.