Bug The Good`ol Asteroid Duplicate Bug

Many of the more stable servers turn asteroid spawning off. The default galaxy size is enough to fund even the more active servers for years between resets.

For your NPC factions do you have server.cfg NPC_FACTION_SPAWN_LIMIT = 0 ? From what I've been told if you have NPC factions they will eventually overwhelm things. Never tested myself mind you. You'll still get pirate and trader ships with that setting off, just no 'faction' ones taking over systems.. One of the initially confusing things about the faction system is the two different NPC types... (which I'm hoping will cease to be with Universe update.)
From what I've read somewhere around the forums, it's my understanding that the scavengers in particular will keep coming to scavenge and basically they don't stop... not good.

I've also experienced the bane that is double roids. There are basically 3 ways to approach it.

1. Turn off roid respawn. Simple but adds travel time as you need to go further and further to get your roids.
2. Turn off roid dynamic physics. This means when they spawn they'll stay over the top of each other. If you can get your players to be aware of them and avoid them or let an admin know when they find them this can work. In my experience it usually means one player may get stuck loading and need assistance to despawn the problem roid near them but it didn't seem to ever bring the server down. Requires an atentive admin.
   
3. Enable roid physics. This means they'll bounce off each other if they double spawn resulting in ping spikes every time they do that usually* resolve themselves but can lead to a bit of time spent with the ping spike. If there's lots of doubles doing this in a sector it can last quite a while and it can crash the server but the plus is it requires less admin time. This option is less appealing if there's lots of people traveling as there's consequently lots of doubles running collision checks.

(note; results may vary depending on server hardware/performance.)
If you do either 2 or 3 then I also suggest you put the spawn time right up from it's default.
ASTEROID_SECTOR_REPLENISH_TIME_SEC = 86400

I got to the stage where every time I logged on I'd /invisibility_mode true and just go to every active player and scan the nav for doubles and remove them. You can see the doubles when they have same size, composition and distance. PITA. Depends on your admin count and activity levels. Established players tend to have less issues but new players or people who travel a lot run into this a lot more often. You may find that setting it up one way works initially while lots of new players are coming on and then when things settle a bit you can change it. Actually while I think about it there is a 4th option of leaving the roid spawn off and turning it back on temporarily to regenerate roids when it suits you.

Empty lines in the server.cfg, never had that before and I would guess it's an indication of an incorrect setting somewhere. Personally I'd be all over that problem first as that sounds like it's got the potential to be terminal.
Always make backups of individual config files before altering them. As well as the backup I (try to) always keep a copy of every file modified so you know what you've changed and don't forget things. This also enables you to drop all your configs into a fresh install and see if a problem like your server.cfg issue is somewhere in your settings.

Best of luck.