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I think that you are confused about the problem here.
The ISA files created for SI do have problems with inconsistent line termination.
The SC_SRCShader Dump section has carriage-return new-line termination (CRLF a.k.a. control-M control-J).
The other sections have just line-feed termination (a.k.a LF a.k.a. control-J).
Otherwise your file looks fine to me.
I think that this has a bug report already.
But in case it doesn't I will file another report.
In the mean time, could you try using a better editor?
Notepad pretty much requires CRLF line endings to work right.
Without the CR's it will display everything as one really long line.
Emacs and notepad deal with this better.
The Visual C++/DevStudio editor is pretty awesome with this -- drag & drop your file there & it will give you a dialog:
The line endings in the following file are not consistent. Do you want to normalize the line endings? <filename>
[Drop down box with 5 choices]
I'll see if I can attach a cleaned up version of your file...
The line termination bug was recently fixed.
The process of fixes making their way to released drivers is somewhat opaque to me.
I'm pretty sure you will see this behavior improved in the drivers that come out in early 2013.
It is possible that drivers will have this fix earlier.