MCP tool calls time out despite server responding instantly when tested tested manually

[mikhail]

Describe the bug

MCP tool calls to a local stdio MCP server (analytics-mcp — Google's official GA4 MCP server) always time out with MCP error -32001: Request timed out, even
though the server responds instantly (<1s) when tested manually via PowerShell by piping JSON-RPC messages to stdin.

The server initializes, lists tools, and returns tool call results correctly when tested outside the CLI. But every tool call through Copilot CLI times out.

Affected version

GitHub Copilot CLI 0.0.420

Steps to reproduce the behavior

1. Install the official Google Analytics MCP server: pip install analytics-mcp
2. Configure ~/.copilot/mcp-config.json:

{
  "mcpServers": {
    "analytics-mcp": {
      "tools": ["*"],
      "command": "C:\\path\\to\\Scripts\\analytics-mcp.exe",
      "args": [],
      "env": {
        "GOOGLE_APPLICATION_CREDENTIALS": "C:\\path\\to\\application_default_credentials.json",
        "GOOGLE_CLOUD_PROJECT": "your-project-id"
      }
    }
  }
}

3. Restart the CLI. /mcp shows the server but tool calls fail.
4. Any tool call (e.g. get_account_summaries) returns: MCP error -32001: Request timed out
5. Testing the same server manually via PowerShell works instantly:

$msgs = @'
{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"test","version":"1.0"}}}
{"jsonrpc":"2.0","method":"notifications/initialized"}
{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"get_account_summaries","arguments":{}}}
'@
$msgs | & "analytics-mcp.exe"
# Returns full response in <1 second

Expected behavior

MCP tool calls should return results within a few seconds, matching the server's actual response time (<1s when tested manually).

Additional context

• Operating system: Windows 11 (10.0.26200)
• CPU architecture: x86_64
• Terminal emulator: Windows Terminal
• Shell: PowerShell 7
• The server (analytics-mcp v0.1.1, reports serverInfo version 1.26.0) uses stdio transport
• Server initializes and responds to tools/list correctly
• The first tool call that worked was via the old flaky MCP package — it returned one result then subsequent calls timed out
• Suspect the CLI's MCP client timeout is too aggressive for the initial server startup/handshake, or there's a stdio buffering issue on Windows

[EvanBoyle]

Thanks for the report. PR is in the merge queue to fix.