Just out of curiosity, I tried if I could reproduce this.
I can, by setting a SVN property on the new file (Explorer file properties / SVN tab / Properties).
Just adding a file 'test.txt' with the word 'test' in it, commit, and diff it from the commit window, launches just my custom diff viewer.
But when I set the property "svn:eol-style" of that file to "CRLF" and then view the diffs from the commit window, it opens my custom viewer showing the file's contents, and TortoiseMerge to diff the properties.
And that's exactly what Tortoise is configured to do in my case: use a custom diff viewer for comparing the file contents, and TortoiseMerge to compare properties.
Could that be what's happening in your case too?
That would reduce the question to: is there anything setting file properties (for example EOL convention) on new files added to your repository?