When a user is promoted with Ontime the groups is added as a subgroup and not as the maingroup. I hope you fix it because DroxPerms is a great plugin and i don't want to change it.

OnTime is closed source. I don't support closed source.

I made changes to Vault which add an option to change the behaviour of the DroxPerms integration to guess if the Main-group of a player should be changed.

https://dl.dropboxusercontent.com/u/16458100/minecraft/Vault-1.2.27-SNAPSHOT.jar

This feature is deactivated by default. To activate it add the Vault.useOnlySubgroups = false option to the DroxPerms config-file as shown in the following file

https://dl.dropboxusercontent.com/u/16458100/minecraft/config.yml

If this solves your problems, then I will make a pull-request to get this change into the official Vault.