Hey Bud i was having teh same problem yesterday with the random missions in my system......If you are like me and using the FLE program to do the system creation...i will give ya a step by step on how i did it
Step 1:
Create a base and determine the faction in control....i only use one faction per base... saves all the weight confusion issues.. also i think i am not sure don't quote me but that difficulty thing for the base i think might have a direct influance to the difficulty of teh random missions...i may be wrong...but if someone knows they'll post it.......
Step 2:
Creat a "zone population" around the base(s) in question....in the encounters add a scout encounter and do the math for the percentages of who is who...for example...the factions...
Encounter type...Area_scout...... 0.50000
Liberty police.... 0.50000
Liberty Rouges... 0.25000
Lane Hackers... 0.2500
this means 50% of the population will be a scout of those 3 factions 50% of the time the police, 25% rouges and 25% hackers....
add what ever else you want to in the population for the other 50% of the encounters.....
Step 3
Add the mission target zones.....viggnet or what ever they are called....
( now this maybe just me but i added a zone population of 1.000 area_scout encounters in the zone with a faction like the Rouges just to make sure the missions would target in that zone and have ships to target)
Thats all i did to get the missions to work....sadly i have yet to figure out how to add extra factions to my bases but for now the missions work well
i was soo pissed about this for the past few days so i am kinda gloating about my triumphant victory over this silly and aggravating issue....thanks to other modders though and their great advice...
i hope it works for you good luck i hope to hear it did