When I draw Pixels with Alpha they don't retain their proper value. To Reproduce in Paint.NET 3.36:
New Document
Select All and Clear
Select the Rectangle Tool
Select Draw Filled Shape
With the Colors Window select ARGB 65,255,255,255
Draw a Rectangle
With the Color Picker Tool sample the rectangle just drawn
You will get an ARGB of 65,254,254,254 so all the RGB values are 254 instead of 255