The transform presets are saved in the presets directory, in the application folder. For example Users/Documents/Maya/2011/presets/attrPresets. Once you have a preset created through the UI, the transform preset will be saved there automatically.
When you save the presets with user added attributes through the UI, the mel script will list them, but will not actually add them since this is just a MEL script that blends the attributes. You can add the attributes in it and they will be loaded next time you use the preset.
So for example:
addAttr -ln myNewAttribute;
blendAttr "myNewAttribute" 0;
The newly added attributes are then available next time you use the presets.