I thought this was because it was running each sub-module individually (instead of using the parent pom) but when I configured it to only have a .lift.toml file in the parent folder it still returned these results.
We have identified the problem, and have a fix. We need to complete going through the review process to ensure everything is solid and then we will be able to make a release for you. My expectation is to have the fix deployed by the first half of next week.