Summary

Setup Bamboo on Windows system with NTFS filesystem
Create Bamboo home folder and remove Bamboo user from permission list (for example leave only group which Bamboo user belongs to)
When Bamboo first time tries to initialise SecretEncryptionService it stores cipher part to filesystem to BAMBOO_HOME/xml-data/configuration/cipher. When this folder created Bamboo removes all existing permissions and leave only owner. In case owner is not in the list of ACLs Bamboo removes all existing ACLs and can't have access to this folder anymore.

All activity which requires SecretEncryptionService don't work

Workaround

Add Bamboo user explicitly to BAMBOO_HOME folder ACLs