Hey, thanks for the detailed report. This is a known issue. It’s a race condition where the tool descriptors don’t get written on the first connection because the tools cache is still empty at the moment of the first write.
A similar thread was here: MCP tool schemas not populated to file system MCP tool schemas not populated to file system for Agent context - Agent cannot discover available tools. One user confirmed a fix in a newer version, but another said the issue came back. So it looks like a regression.
For now, the only reliable workaround is toggling it off and on, like you already found.
The team is aware of this problem. Your report helps with prioritization, and it’s especially helpful that you captured a clear pattern 64-tool FastMCP, Windows, and metadata timestamps. I’ll update here when there’s news.