Custom Type not recognized with `instanceof`

Describe the bug

I'm using instanceof to check whether a variable is an instance of a custom SignatureError class (class SignatureError extends Error).

This check works correctly when running the code directly with Node at runtime, and also when using the Node test runner.

As pointed out in a previous issue on fastify/fastify-autoload (https://github.com/fastify/fastify-autoload/issues/472#issuecomment-3057127685),
the issue might come from module cache inconsistencies due to different import paths:

the import cache is considered the relative and absolute path of the same module as two different file.
You can observe we are using dynamic import with absolute path, and you are using relative path.

Additional context

• This issue is similar to https://github.com/vitest-dev/vitest/issues/3676
• Might be related to https://github.com/vitest-dev/vitest/issues/4559

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• Follow up of https://github.com/fastify/fastify-autoload/issues/472

Reproduction

Code: https://github.com/marcalexiei/fastify-autoload-vitest-instanceof-bug

GitHub action run: https://github.com/marcalexiei/fastify-autoload-vitest-instanceof-bug/actions/runs/16197482983/job/45727664415

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The SignatureError class is always imported from the same file:

• https://github.com/marcalexiei/fastify-autoload-vitest-instanceof-bug/blob/main/src/SignatureError.ts

it's used in:

• The instanceof is in src/app.ts
• The error is generated in src/routes/debug/index.ts.
  This file is not explicitly imported. It is loaded dynamically by fastify-autoload in src/app.ts:

System Info

System:
    OS: macOS 15.5
    CPU: (12) arm64 Apple M2 Max
    Memory: 5.34 GB / 64.00 GB
    Shell: 5.9 - /bin/zsh
  Binaries:
    Node: 24.3.0 - ~/.nvm/versions/node/v24.3.0/bin/node
    npm: 11.4.2 - ~/.nvm/versions/node/v24.3.0/bin/npm
    bun: 1.0.17 - ~/.bun/bin/bun
  Browsers:
    Chrome: 138.0.7204.93
    Safari: 18.5
  npmPackages:
    vitest: ^3.2.4 => 3.2.4

Used Package Manager

npm

Validations

• Follow our Code of Conduct
• Read the Contributing Guidelines.
• Read the docs.
• Check that there isn't already an issue that reports the same bug to avoid creating a duplicate.
• Check that this is a concrete bug. For Q&A open a GitHub Discussion or join our Discord Chat Server.
• The provided reproduction is a minimal reproducible example of the bug.

Run the linked minimal reproduction first, then inspect src/SignatureError.ts, src/app.ts, and src/routes/debug/index.ts, including the dynamic loading path through fastify-autoload. Trace how Vitest resolves and caches the module in this scenario. Done means the reproduction's instanceof check recognizes the generated SignatureError under Vitest without regressing the Node runtime or test runner behavior.