Been having similar issues on my dedicated server as well, haven't been able to nail down exactly what's wrong. My missions do start eventually, sometimes taking up to 5 minutes to start.

Try double checking every single module and make sure that there are no user made errors in the module configurations, like wrong marker names for TAORs and Blacklists or redundant CQB modules. Worst case, redo all the objectives and CQB modules one by one, and make sure the missions loads normally after each one.

The yellow dots are a debug feature, they only show up in a singleplayer/editor-started mission.