Hi Joe,
The text-layers will dynamically resize themselves per the text size used when editing them, and any manual rescaling of the layer will be replaced. The best thing to do is not rely on manually scaling text-layers and instead only use the text size parameter while the text-editing mode is enabled to get it to the scale you want, and let PixelCNC determine the size of the layer for you.
The ability to manually scale a text-layer is really only meant for fine-adjustment when the text will no longer need any further editing - which includes changing the font and character spacing. :]
- Charlie