In either 3.8rc2 or 3.8rc3, at a shell prompt, I get the expected PATH:
Its only in emelfm2 that I see the difference. I don't see any config files getting created at extension load time, but shouldn't they be the same anyhow?
--- a little time passes, during which I do some testing and roberts does also ---
I'm not a rox-filer user but I was able to verify that this issue affects rox-filer as well. I also determined that if I close down X completely (exit to prompt) and restart it, the symptoms disappear.