I remember there was a NullPtr issue with the ByteBuffer allocation that I already fixed. That issue I however have long fixed on the vscode branch. Is it the master branch you downloaded? There I still get an error on the mod.lst file for some of my saves and I remember that was NullPtr related.
If still facing that issue, with Eclipse try update the gradle project or re-import it. Else run the 'clean ' task and delete bin folder on disk, then rebuild.
If that doesn't help, upload some saves to check and tell on the mod. With vanilla and AAML I'm not facing such issues. At least not with vscode branch I'm working on and waiting for DCER to merge it to the master branch.
Edit: I however just fixed another bad issue where I ran into a deadlock when switching to map view after performing integrity checks or vice versa.