MCP servers from org registry disappear after working — false "disabled by organization" warning (v1.0.11)

[dowsn]

MCP servers configured via our organization's MCP registry were accessible in GitHub Copilot CLI approximately one week ago. They are now gone, and the CLI shows a false warning on startup:

! Third-party MCP servers are disabled by your organization's Copilot policy. Only built-in servers are available.

No such policy exists. The same MCP servers from the same org registry are visible and working in VS Code Copilot Chat.

This is different from #1707 — the issue is specifically about org-level MCP registry servers disappearing after previously working, not just a false policy message on locally configured servers.

Environment

• Copilot CLI version: 1.0.11 (latest)
• MCP configuration: Org-level MCP registry
• VS Code Copilot: Same registry servers work correctly
• OS: Windows / WSL2

Affected version

1.0.11

Steps to reproduce the behavior

1. Configure MCP servers via org-level MCP registry (same as used by VS Code Copilot)
2. Start GitHub Copilot CLI v1.0.11
3. Observe the false "disabled by organization" warning
4. Run /mcp — registry servers are not listed

Expected behavior

MCP servers from the org registry should be available, as they were ~1-2 week ago and as they currently are in VS Code Copilot.

Additional context

• Appears to be a recurring regression: originally reported for v0.0.418 (#1707), re-appeared in v1.0.3, still present in v1.0.11
• The org-level "MCP servers in Copilot" setting is Enabled at https://github.com/settings/copilot/features

[nioertel]

Same issue here

[vmagalhaes]

Same here

[tfriesenbccorp]

same and very annoying. hoping for a quick resolution.

[ai4adesso]

It happens also under macOS

[HillLiu]

when make it allow-all, but still show "! Third-party MCP servers are disabled by your organization's Copilot policy. Only built-in servers are available.", and mcp get stop work...

[ai4adesso]

v1.0.12 seems to have solved