The profiles were made years ago when the experience ranges were much larger.
Now that the experience is hugely nerfed - less quests are needed for you to level which is why you're ending up as 69 in Nagrand.
The questing botbase runs off of a checkpoint system that has it skip quests.
However, the checkpoint system isn't checked until you stop/start the bot or until it reaches a checkpoint in the profile.
If you stop and start the bot - and you have "Ignore Checkpoints" turned off, then you'll see it skip quests (assuming the profile you're using utilizes them.)
EchoTiger wrote up a solution for having the bot stop->start every time you level up so checkpoints are constantly checked, but I don't have the code right now.
He also said that there's a feature request on the internal tracker to have a "check checkpoints on levelup" option on Honorbuddy, so hopefully that'll be out soon.