All of the above is from conversations with Doug Murray, who's more or less responsible for getting all of these detailed varieties into the latest Friedberg. The original seal (with the solid background behind the shield) was used for much larger quantities of the higher-denomination notes--for example, on 1862 $5's the seal change occurs in Series 59. But the $1 and $2 went into production later than the other denominations, and each of them had just a few thousand notes printed before the new seal came along.
I am going to have to reread these posts about 50 times before some of it starts to stick. I still need an 1862 for my one dollar type set.