I've created a .PNG watermark file 600x50, duplicated the export preset JPEG Original size and edited the preset as follows:
- ticked Show Watermark,
- set the Position to Lower Right
- Opacity to 50%
- chosen the .PNG file (which Aperture has copied across to its Watermark Images folder)
- I have left Scale watermark unselected.
The duplicated and edited preset has been saved and comes up whenever I chose File, Export, Version.
The export creates a JPEG copy as expected, but no watermark is added.
Might it be too small? What size are your JPG's? You are exporting at original size, and your watermark is only 50 pixels in one dimension (unless that's a typo).
Try exporting to an image size of 600 x 600, and set opacity to 100%. This should confirm whether your watermark is being used.
Then you can trouble-shoot either:
. the watermark is not being used, or
. the watermark is not giving me the result I expected.