Adding an image to the Atlas Builder which resides in a folder path containing spaces causes the path to the image to be stored in the ATL file's <ImagePath> element with '%20' instead of spaces. Such files will not load back into the Atlas Builder as it complains it cannot find the image - manually converting the %20 to a space in the ATL file using notepad fixes the problem but it comes back as soon as the file is re-saved
For Example the folder structure:
\Project\My Atlas Folder\MyAtlas.atl
\Project\My Texture Folder\AtlasImage.png
will cause the <ImagePath> element to be "..\My%20Texture%20Folder\AtlasImage.png" which will not load back into the Atlas Builder.