@SYN_Bliss
Thinking of ghost planes... Are those dots actual aircraft or only dots, i.e. can you switch to them if you have external views on?
In case these are actual aircraft this may be a script issue. Script may destroy (remove) actual aircraft from server. If this is the case you could post the script in fmb section
http://forum.1cpublishing.eu/forumdisplay.php?f=203 to let someone like TheEnlightenedFlorist or FG28_Kodiak to fine-tune it if needed.
Connected to your server yesterday. There were many bomber formations visible (like 7 or 10) at the same time. There were only about 8 players at that time and it was hard to find any human players because everyone could go into different direction pursuing different formations. I think the mission could become more dynamic if action is concentrated in one area. To achieve this I would suggest loading only 1 submission per 30-40 minutes (max 2 groups of bombers, 1 per side) and print on screen and in chat where the action will take place. Just an idea.
Another suggestion is mpdotrange settings. My personal opinion is the dots now do not seem realistic enough to me because mpdotrange DOT is set to 20 or 25.
Checked Repka 1 yesterday as well. There are no ghost planes there. Thus I do not think this in a netcode issue. Repka mission has 3 submissions loading every 40 minutes. And 2 submissions loading every hour. No more than 4 small bomber groups can be found in the air at the same time. The mission can be found in the missions thread in this section. Please feel free to try it on your server to exclude the possibility that ghostplanes could be caused by a mission.
Taking into account you server hardware I think you can run 2-3 servers on it if you create virtual PCs like BigRepa does for Repka 2 and 3. One of them can be used as a test server then.