The fix for bug #16 (duplicate checkpoint serial numbers) will be integrated into ION version 3.2.0, but in the meantime here's a patch for version 3.1.2. To apply the patch:
1. Download bug-0016.patch from here.
2. Copy it into the ion-open-source top-level directory.
3. cd ion-open-source
4. patch --unified -Np1 < bug-0016.patch
5. Then remake.