OK, it seems I found the problem: new lines.
I just took a file I created on Linux, used Source Formatter and it worked. Now I converted the file using unix2dos, opened it again, used Source Formatter and got something just like the code you pasted in your first post.
I'll try to find a way to fix that. I still need to update the plugin to a more recent version of AStyle anyway.
[edit]
OK, it's fixed now. Updated to AStyle 1.20.2 too.
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