I ran into a similar issue and it turns out to be a problem with "File Vault" tool provided by Jackrabbit. The version of the tool I had the problem with was 3.1.18 and I had to either degrade to a previous version (3.1.16) or get a more recent build (3.1.42). To be 100% the issue comes from this tool you can:
1) install fileVault in your system (expand the tools from AEM_HOME/crx-quickstart/opt/filevault into any other folder you choose) and configure your PATH to also include this application
3) using "vlt" command do a check out
4) modify some content in the file system and do a check in
5) modify same content using CRXDE lite and do an "update"
6) take a look into .content.xml files and see if there are properties missing, if so, we are 100% sure the issue comes from the file vault version you have. If not, we need to look into other things.