The _flushRoutingTableCacheUpdates command can fail if run right after startup. This is because _flushRoutingTableCacheUpdates requires a key in the key cache to correctly work. However on startup, the key cache is empty and the KeyCollectionManager which periodically refreshes keys into the key cache is not guaranteed to be run by the time _flushRoutingTableCacheUpdates is run. 

I think the easiest solution is just to have the retry_on_transient_error_basic.js retry the _flushRoutingTableCacheUpdates command if it fails (via assert.soon).