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I've created a new layer filled  with Transparency. Made it active by clicking on it.
Go to the Rectangle Select tool. Draw a rectangle on the canvas.
As soon as I click on any other tool in the Toolbox the rectangle I drew disappears off the canvas.
I've created the rectangle with all of the Modes. Same results.

What didn't I do?

Jim

1) Make sure the selection is visible at all times, View>Show selection should be checked (you can also hit Ctrl-T a couple of times to see if this elicits the marching ants)

2) in some cases you have to "commit" the selection (double click in it, or strike Enter) tp make it stay.

Thanks. That seems to work.