Could you post the output_log.txt file (default location is in C:\Program Files (x86)\Steam\steamapps\common\Pillars of Eternity\PillarsOfEternity_Data). If you could try to add Aloth, and grab the output log file then, it'd be great. It sounds like exactly the same problem, indeed. But because it's (also) Aloth for you where it was primarily Hiravias for others so far, seeing what it records in your output log would likely give more information on what exactly went wrong (beyond the general "wrong files coming through the Steam installer", which seems to be the root cause).
Here's the output.log
It appears that certain conditions determine whether I can assign Aloth (and other companions) to party. My long time party consists of Eder, Aloth, Durance, Kana, Sagani and myself. If I dismiss any number of these "original" companions I can reassign them normally. But if I try to take Grieving Mother and Hirivias same time only the GM actaully is assigned and Hirivias can be seen in your party only in party management screen.
Steps I did before grabbing output.log:
1. Start game, load save in Caed Nua
2. Go to party management and dismiss Kana and Aloth
3. Accept
4. Go to party management and assign Grieving Mother and Hirivias and Accept
5. Notice that Hirivias is not in party but he can be seen assigned to party in party management window
6. Dismiss Hirivas who is not actually in your party and assign Aloth instead
7. Accept
8. Notice that Alot is not in your party
These steps alone does not seems to work every time though. I clicked GM and Hiravias in different order to assign and dismiss them multiple times and sometimes I got them both, sometimes, only one of them and sometimes neither of them. Hope this information gives some clues about what's happening. Feel free to ask more.
output_log.txt