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Have you registered each of your DSS filter output files against each other? If your using Photoshop it is much simpler (and quicker) to align all these files before taking them into Photoshop. I can't speak about how PI does it or what it needs as input, you will need to consult the Cult for that info.
The DSS layering alignment is pretty simple:
Open DSS, and pick up each of your stacked and registered filter output files. Tick the option to "Register Already Registered Files", this will ensure these output files are registered against each other. Also tick the "create a REQ file", this will then create an aligned (registered) file for each channel (which gives you a working output file for Photoshop) It runs quickly.
Then in Photoshop, open the REQ files for each filter channel, and convert the mono file to RGB, you can the go ahead with your stretching etc. I usually work to equalise the histogram for each filter. Once your happy with the individual filter files, start your colour layering.
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