To see the issue follow these steps.

Draw a rectangle any solid color.
Apply a 16pix outline
Apply a flat 50% transparency.
With GNOMRA on... draw a new rectangle
Remove the fill color by selecting the hash (no color) box in the color bar.

What you have is a rectangle with a transparent outline.
Click on the Transparency tool and what do you notice? There is no transparency applied, meaning it can't be removed. This is true even if you reapply a fill. There is still no transparency applied and it cannot be removed.

I'm not sure, but I don't think that this is expected behavior.

Eric