I do not see any special in your logs provided. There are same info about following leader in both parts.
To test out what is your problem, you need to do exactly same environment: i.e. should be same dungeon, same place of dungeon, and ofc same team.
If any of this not same (i.e. further of dungeon place or bot stop\started manually in dungeon run), it's not clear test and as results as your determination of it most likely wont be not correct.
You can do this test by:
1) Run via DungeonBuddy only (from start of dungeon, not part etc) -> i.e. clean full run.
2) Run via GoldBoss -> BotManager -> DungeonBuddy (from start of dungeon, not part etc) -> i.e. clean full run.
3) Compare results
p.s. stream of all other HB Products should be disabled in BuddyStore before run, to exclude their influences
Not following issue, should be not connected to any sort of GoldBoss, but can be connected to concrete circumstances of specific Dungeon \ RAF settings for Followers toons.
You can have same behavior (not following and suddenly started following again) - after you stop/start Honorbuddy manually (without changing BotBase) - it can as well run than smoothly after it (in this case it's something internal).
As for GoldBoss, you should understand - it do not manage what exactly BotBase, which are you using (i.e. DungeonBuddy), doing, do not gives commands in any sense to it, so what/how to do is up to BotBase.
So, totaling, I can only propose you to PM me with your skype name or poke me on Discord to test it with you online via TeamViewer.