Perks not getting fully restored after Tranquility Lane

[kyods]

Hello, 

I've just run into an oddity - I've looked at the forums and the bug tracker, but couldn't find anything relevant. It seems that certain perks are not fully restored upon exiting Tranquility Lane. This seems to apply to quest and companion perks - perks gained during level progression work fine.

Before I entered the lounger I had a +25 lbs bonus from Strength Bobblehead, and +1 PER and +25 Fire Resistance being a quest reward from These!. Upon exiting the lounger I noticed that my carry load bonus, fire resistance and perception bonus are gone, even though Ant Sight is still listed as an active perk. I re-tested, this time switching from an FCO race to vanilla Caucasian race, result was the same - I had to manually re-add Ant Sight to get the actual bonuses back. I'm not really sure at this point how to re-add the 25 lbs carry weight bonus.

I've collected another Bobblehead granting me 25% more durability for my items, but I'm not exactly sure how to check whether this bonus has been restored.

I also tested this with a custom follower who adds a custom perk combining Jury Rigging and +10 Repair. Jury Rigging was re-added correctly upon exiting the lounger, there was no trace of the Repair bonus though. Curiously the same thing happened when I dismissed the follower, losing the perk, then re-hired them - I got Jury Rigging back, but not the repair bonus.

My specs:

i7 4770k @ 4.4 GHz, 16 GB RAM. Windows 10 Anniversary Update. FOMM 0.14.11.12. I have Steam GotY version of F3.

Install log and load order below.

[RoyBatty]

Ideally we would need Risewild to test this. He is currently unable to do so however. I can try to test this later if I remember to do it.

[anstand]

Did you restart the campaign after the race change or did you change that during the game?

Because if you change the race during the game (showracemenu), you will lose all perks to begin with.

[kyods]

I did not restart the campaign, and all my perks were still listed as active (and I'm pretty much sure they actually were active after showracemenu). 

The problem with the companion's perk getting restored only partially upon re-hire happened while playing as a vanilla race, without any prior race changes since the beginning of the game.