Ok, my $0.02. Though in the current position, your daughter's skills and the organization's mission might be a match, the management doesn't seem to be. People leave (bad) bosses far more often than they leave jobs. If the VP at the top of the non-profit chain of command is the terrible boss s/he appears to be, any position in that organization will eventually become unpleasant. Thus, of the two options on the table, the other, more stable job which presents more choices in bosses as well as retirement savings seems to be a better choice. Now, if she "loved" the current job and had a great boss, that would be a different matter altogether.
As for bringing adult children back to the nest, I'd recommend doing so only after agreeing up front to some modest amount of rent and well-defined household contributions. Nothing better than putting expectations in writing to get off to a good start and stay on track, in my mind! Any rent collected could be placed in a savings account for the child's future benefit, perhaps for a down payment on an apartment or home. Then again, I charge my 7 and 10 year old kids rent, which they pay using allowance earned for chasing dust bunnies, making their beds, setting the table and loading the dishwasher....