Do you run multiple threads in your game? Artemis is single threaded, so when dealing with multiple threads you need to synchronize, or better compartmentalize, access to artemis - if that is the case.
Vanilla artemis was a little flaky when it came to creating entities during an ongoing process loop. Sounds like it might be what's causing it, though I don't remember seeing your particular problem. Worth a short anyway.
The Underkeep and Naturually Selected 2d both use gradle - they're too.
-
https://github.com/DaanVanYperen/naturally-selected-2d-
https://github.com/DaanVanYperen/underkeepEdit: artemis-odb should be fully API-compatible with vanilla (up until when/if artemis-odb 1.0.0 is released - but I'd rather avoid breaking compatibility).