Enfuse creates an empty Alpha Channel which in Photoshop CS4 pops up in the channels as Alpha 1.
This means that if you need to create an alpha channel for example for the nadir you have to remember to save it as Alpha 1 to exchange it with the already existing.
However CS5 does not read the Enfuse channel as a channel but it opens the image as a layer.
It does not seem to make any difference besides creating a new alpha channel just needs to be saved as new.
PTgui does not mind that the images are not flattened and if you save the alpha mask as a layer mask it works just as good besides that my 16 bit Mark II images becomes 370mb instead of 160.