I cannot place any blocks when vault is running on my server. Please help. I am using version 1.4.1 but I have tried older version and it still dose not let me place blocks.

Vault doesn't do anything related to block placement. You most likely have something that is hooking into Vault to check for permissions and it's not seeing you have some specific permission. For information on what Vault actually does please see the readme on the frontpage, or the information where you downloaded it from. https://github.com/MilkBowl/Vault/