I also had that issue and I've tried to find out WTF. I have 4 characters; let them be
Ch1,
Ch2,
Ch3,
Ch4.Ch1 is the oldest character. It was created few days after the release. It survived all the patches and still had no issues with random dragons.
Ch2 Was created just before the 1.2 patch. It was a mage and it had faced the issue of disappearing random dragons.
Ch3 &
Ch4 were created after the 1.3.7 patch.
Ch3 is a mage,
Ch4 is an archer/warrior. I played them both one after another so recently they both reached the level 40. And then the problems began with
Сh3. Random dragons disappeared once again. I tried to change the variable
enabledragons. It doesn't help. If your random dragons are OK it doesn't make them dissaper. If they are broken it doesn't fix them.
Just because I had several characters on my PC which had no issues with random dragons, I realized that the uninstall/install would not help. I tried to load the previous saves of my
Ch3. I had several of them: on lvl 37, lvl 33 and lvl 30. Because I had random dragons and suddenly they disappeared I decided to check the circumstances of that issue. I compared the progress on different quests with my
Ch3 (lvl 30, lvl 33, lvl 37) to find out what’s wrong.
Just a few word about the test: I use the fast travel up to 20 times one after another. If your random dragons are OK, you will meet one of them within 10 +/- 1 fast travels. To be sure, I used fast travel up to 20 times.
That’s what I found. The saves on levels 33 and 37 for
Ch3 were broken also. No random dragons. But the save on level 30 was OK. After 20 fast travels I’ve met 2 random dragons. I’ve compared the progress on different quests (also I tried to remember the progress of the
Ch2). That’s what I’ve found:
1) Archmage. It is not essential for random dragons to disappear, but somehow important. Ch1 and Ch4 had not complete the College of Winterhold questline and do not have this sort of issue
2) J’zargo’s experiment. It is most likely to cause this issue! Ch3 lvl 30 killed only one undead with J’zargo’s scroll, while Ch3 lvl 33 has already 3 undead killed (but still didn’t report back). Also Ch1 and Ch4 didn’t even start this quest. Also as far as I remember Ch2 had complited this quest just after becoming the archmage.
3) The horn of Jurgen. The difference between Ch3 lvl30 and Ch3 lvl33 is in the progress on the main quest. Ch3 (33) has met the Greybeards while Ch3 (30) hasn’t. It may cause the disappearing dragons issue but only in certain conditions because Ch1 and Ch4 have met Greybeards, found the Horn and still had no problems with random dragons.
Anyone who had the same issue, please check the progress on these quests. It is possible that the problem is really in the progress on different kinds of quests and their combinations.