I highly recommend using database for storage instead of flatfile when using MCClans on a live server. Flatfile is intended only for testing or checking out the plugin.
The database storage option stores changes immediately. Whereas the flatfile storage option only does so when the server cleanly exits (not crashes). But I'll take a look if flatfile is still working normally on this version as you say it also goes wrong on a clean restart.
Steps for switching from flatfile to database:
1) Set up a MySQL database.
2) Create a backup from your data using
/clan admin backup (just in case).
3) Stop your server.
4) Go to the config and configure the database section.
5) Copy the four json files from
data/load. What this does is trigger MCClans to load the data from these files even though it is configured to use a database.
6) Start your server, and check the logs for warnings to see if the database is configured correctly. If it's not, repeat from step 3. If it is, your files from step 5 will be loaded in and converted to the database.
If you need any assistance with this let me know.