Not quite sure in waht sense you mean ID is not recognizing the alpha channels. Can you explain more, please? I'm certainly able to use A photoshop CS6 alpha channel as a clipping mask in CS5.
As far as bug fixes, if there really is a bug (and I don't have any reason to doubt Chris Cox), it's pretty unlikely that there will be any patches issues for CS5 or earlier at this point.
The images in question all use alpha channels to mask out the image backgrounds (usually white) in InDesign layouts.
I opened the images in PS6 to crop out excess background (to get file size down) and saved the new files.
When I go to import the images one by one into InDesign 5 (via Cmd-D, Import options ticked) the Alpha Channel pull down menu is greyed out and I'm unable to select the Alpha Channel.
If I open the image in PS5 and resave, I'm then able to access the Alpha channels in ID5... but that's a lot of images to go back through to fix.
I also tried opening the layout in ID6 (where the alpha channels do work) and saving down to the idml format. When opening up in ID5 the alpha channel is no longer recognized and the background of the image that was masked out is now visible.
OK, I see that with tiffs, but not with .psd. Why not batch save the files as .psd?