I suspect that you're seeing the results of changes in friction properties as the rims warm with brake heat. Squeal usually only happens on gentle braking, where the forward force of the rim can push the pads forward and twist the brake arms. Then they slip back, this repeats and becomes an oscillation which you feel as shudder at low frequency or hear as squeal at higher frequencies.

You rarely hear squeal at higher braking forces since the higher pressure holds the pads flat against the rim and prevent the twist.

Possibly as the rim warms and the pad material softens, the coefficient of friction rises, and you unconsciously ease back a bit allowing the squeal. Give it some time, and it might self-resolve, or become less frequent. For example, my commuter bike's brakes only squeal on certain days when the humidity is just right. So while you might complain about squeal, I have a nifty rolling hydrometer.