What kind of role do you think the Freys played during First Blackfyre? Did they totally support the Blacks? Or did they hedge their bets & provide half-assed support? Or sat out all together? They are not listed anywhere as one of the top Black Houses, nor did Ser Eustace list them among the half-supporters. Yet Lord Peake seemed very sure of their support during Second Blackfyre.

The Freys’ presence at the Tourney of Whitewalls suggests they had either “fought for the Black Dragon once,” or had “reason to resent Bloodraven’s rule, or nurse grievances and ambitions of their own.” Given their prominence in the whole affair, I lean to the former rather than the latter. 

As you say, Ser Eustace doesn’t name them among the Houses that tried “to keep one foot in each camp” or as having outright betrayed Daemon like the Lothstons. So I would guess they fought straight-up and then bent the knee. As for why they’re not numbered as one of the top, they’re a lesser House and nouveau riche to boot.