War Commander is what's called a "Client Authoritative" game.
This means that the game takes place on your computer, then sends the results of your gameplay back to our servers. Problems like this occur when packets of data are lost or mixed up in transit from the player's system to the server. In this situation, your final commands--the ones setting your repairs--aren't making it to our server.
When you bank resources, deploy a platoon, switch between the world map and your base view, and/or recall a platoon, your computer automatically tries to send the most up-to-date information to the server. If you make sure to leave the client open for a few minutes, then the server should have plenty of time to receive the proper information. This is easy! The following steps should prompt a base save and give your commands time to make it to the server. If you have repairs to do while you're offline, we encourage you to take these steps right before every sign-off:
1. Set whichever platoon you wish to repair
2. Wait for the save icon in the top right corner to turn from red to gray
3. Exit the storage or platoon window
4. Bank your resources to trigger another save, or visit the world map, then return to your base view
5. Wait for the save icon to turn from red to gray once more. Wait a full minute to ensure the packet exchange is complete.
6. If you are done, log out. Adjusting your repairs again means you will need to repeat these steps.
*Note: If you do not log in for 48 hours, your repairs will stop. This is an intended feature; be sure to login at least once every 48 hours to prevent those repairs from stopping.