When submitting a config command to the flume master, it seems as if the downstream node attempts to load the config twice.
In a test case, starting a single master and a single node, I submitted a "config node rpcSource(12345) console". The node sees the config change on the next heartbeat and updates its config and starts the thrift source on port 12345. Immediately after, it logs "Taking another heartbeat" (DEBUG) and attempts to create another logical node with the same config. This leads to thrift errors in bind() and "Could not create ServerSocket on address ...". Looking at the root cause in a debugger (thrift swallows the original exception) I can see it's an "Address already in use" IOException.