I found that Buildship does not respect the defined “Gradle User Home” within Buildship preferences when converting an Eclipse project to Gradle nature. This is in contrast to importing an Eclipse Project (with a gradle.build file) as Gradle project. It falls back to the default to the user home directory (which I do not want).
Thank you for the report! I can reproduce the issue. The fix is trivial, so a likely candidate for 1.0.18