The error message appears if the disk or partition where agent's storage folder is kept, has only 1Gb or less of free space left.
Note, the error message refers to the disk where agent keeps its setting, not to the disk where files are synced!
It's highly advisable to free up some space on the storage. Otherwise, agent may encounter Database error or fail to save it's current configuration.
Error code SE_RUNNING_OUT_OF_FREE_SPACE