Intermittent MCP tool call failures with unexpected permission prompt

Occasionally, MCP tool calls fail with the following message:
```
Claude requested permissions to use mcp____, but you haven't granted it yet.
```

If I repeat the exact same request, the tool call then works normally.
This makes it seem like permission detection is inconsistent or not persisting correctly between requests.

My Current Options Configuration
```js
options: {
betas: ["context-1m-2025-08-07"],
allowedTools: ["mcp__"],
disallowedTools: [
"mcp____exclude_tool_one",
"mcp____exclude_tool_two",
"Bash",
"BashOutput",
"Edit",
"ExitPlanMode",
"Glob",
"Grep",
"KillBash",
"KillShell",
"LS",
"MultiEdit",
"NotebookEdit",
"Read",
"Skill",
"SlashCommand",
"WebFetch",
"Write",
]
}
```

This happens once in 10 or 20 times.