Hmm. How do I check to see if the alpha is constant throughout the duration? And do you mean "current layer" under "source"? Once I sample a piece of the frame (holding option) it automatically switches to the name of the layer I'm working on.
My settings are Mode: normal, Channels: RGBA, Duration: constant, source: name of layer I'm painting on
As I said, this behavior is typical if the layer already has an Alpha channel and it changes over time, i.e. it is a clip or image sequence with Alpha. Other than double-check the brush and paint settings. Also make sure you do not use otehr masks and effects on the layer that may be selected in the layer display box in the right bottom corner...
Thanks for your replies, but it's not any of those things. For example, if you take a jpg, no alpha channel, no masks, just in a clean comp by itself and paint a clone stamp stroke on it and then check "paint on transparent," the whole layer disappears. Whereas with a normal, non-clone paint stroke it will turn off the BG but keep the paint.
If it matters, the point of my wanting to do this is using mocha, mocha import, and RG warp to stabilize shots for painting out wires and rigs. It wouldn't be an issue except that this combination of things results in a minor quality loss so I want to contain it to the paint strokes only.
Actually, I just figured out a workaround while writing this, for anyone who cares: the issue seems to be that you can't use the layer you're painting on as a source layer for cloning. But if you duplicate the layer, open the original in one layer window and the duplicate in another, you can use the duplicate to sample from and paint on the original. Then when you check "paint on transparent" it works as promised.