Looks like your new layer is an empty image...
Let's start over again:
Open your image in mtPaint
Select your image either by pressing CTRL+a or from menu Selection -> Select all
Copy selection into clipboard either by pressing CTRL+c or from menu Edit -> Copy
Create a new layer from menu Layers -> New Layer
This brings up a dialog where you have to tick From Clipboard
Since JPG has no alpha channel you have to add it from menu Channels -> New ...
This brings up a dialog where you have to tick Set
Alpha should be selected by default
Make sure that menu Channels -> Couple RGBA Operations is selected
Press v for the preview
Now edit the layer to your liking
Save the preview image using the menu Layers -> Save Composite Image ...
By default this will save as PNG, but can be changed to JPEG
As another example i edited the image from my earlier post as jpg
I have scaled it to fit into the book cover and then skewed it instead of rotating to fit the angle

- mtpaint-mtPaint 3.50.09 (Modified) Untitled.jpg (52.67 KiB) Viewed 1225 times