Yes, as it cannot read the cert that is stored on your computer. You're in a sandbox.
Due to the isolation of the sandbox, sandboxie provides its own service program. Sandboxie has it own Cryptographic Services(SandboxieCrypto.exe) to manage software signing, security certificates and software catalogs. Any certificate modification are written in the sandbox. By design sandboxie should be handling this.
Any changes, like this, should be done outside the sandbox first. Otherwise, it is not written to your host. This is the purpose of SBIE.
What's the purpose of using sandboxie if you're going to visit the site outside the sandbox. How could it protect you from zero day exploit then.
You can give direct access to your vault, but I would advise against that. If you delete something while sandboxed, then it's replicated to the host. There is no safety net.
You can't make a direct access to that or modify it because it is locked by running service.