Yup, it's a persistent problem that still hasn't been fixed. Best way to deal with it is to log into your server and get it started, then use the check server page to have it re-read the mods. Wait 5 minutes, after that people should restart the launcher and it will usually launch in the right order. It's a shame we can't specify the launch order for mods for our servers. This is a pretty persistent problem and is killing server populations.