I am seeing the same issue and have reported it to SW in the following case:
Case Update: 124759 - Netflow issues during startup
Their response makes some sense, but I believe it is still a bug that they need to work out. Basically, the SW support staff is indicating that this occurs because while the SQL DBMS service may be started, the NetPerfMon DB may not quite be ready so the NetFlow service sees that SQL is running (which is its only dependency) and attempts to start. The NetPerfMon db is not ready quite yet though and therefore the service fails. By the time the NetFlow service tries to restart (since recovery option is set to restart on failure) the db is fully ready and the service is able to start successfully.
I believe if SW can either increase the timeout while waiting for the DB response or set NetFlow as the last SW service to be started this may resolve the problem. Additionally, if your server is just a bit beefier, you probably would not see this issue.