Duplicates viewer can not display results

We have a build script that generates IDEA projects as .idea directory.  As it looks like TC does not recognize directory-layout projects, I extended the generator to create IPR, referencing the same modules. Now the Duplicates analysis runs successfully, the summaries are fine, but the actual file paths are weird. I assume it might have something to do with our project layout.

Since the summaries are ok, I assume it's an issue with the Duplicates XML report generator. Could you confirm please? Shall I create a JIRA issue?
I'm attaching the build config, a screenshot and the generated project files. Let me know if I can provide anything else.

Also any tips on how to change the generated project would be appreciated (I've tried absolute file locations - same result.)