EOL errors when using merge

I am encountering problems with conflicting EOL characters when merging
from Trunk to a Feature branch. The files in both the Trunk and Feature
Branch have Windows-style CRLF EOL characters, however, when I merge,
certain files appear as having conflicting EOLs. I did try the ignore
EOL option as well as ignore all whitespace, however, still some files
appear conflicted and the diff tool seems even more confused (the
attached PNG is for this ignoring EOL/whitespace case, where I get this
section of orange and question marks in the merged copy.).
 
Any ideas on what could be going wrong here?
 
Thanks,
-Paul
 
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