While leveling a PC Ranger, the player mulitclasses to Order of the Bow Initiate (OotBI, homebrew implemented, class is from Complete Warrior p68), although I doubt it matters what class is used. The current level of the PC is 8: Ranger 6 / OotBI 2.
The noticed issue is that the Ranger's animal companion (wolf in this case) has been leveled to 4 following the total PC level and not that of the Ranger level (6). Which, in this case should keep the wolf companion at level 3.
Windows 7, PCGen 6.02.1
I'm sorry, I completely misunderstood your issue. I hate to say it but this is going to be beyond our ability to 'fix'.
See, we don't have 'Complete Warrior' from Wizards of the Coast as a set we maintain or support (License restrictions). I initially thought this was a Pathfinder issue, hence the hasty request to have you open an issue so I could investigate and fix it later.
I'll contact you off-list to discuss the options available. However, we have no method to officially address this as any official support for CMP sets was lost when CMP's license expired (Around 2008 IIRC). Frankly, I'm surprised you have a set that even works in 6.02.1
Closed Content issue beyond our capability to address.