exclude directive is ignored in flake8 3.4.x (regression from 3.3.0)

{
  "dependencies": [
    {
      "dependency": "setuptools",
      "version": "36.0.1"
    }
  ],
  "platform": {
    "python_implementation": "CPython",
    "python_version": "3.6.2",
    "system": "Linux"
  },
  "plugins": [
    {
      "plugin": "flake8_quotes",
      "version": "0.11.0"
    },
    {
      "plugin": "mccabe",
      "version": "0.6.1"
    },
    {
      "plugin": "pycodestyle",
      "version": "2.3.1"
    },
    {
      "plugin": "pyflakes",
      "version": "1.5.0"
    }
  ],
  "version": "3.4.1"
}

Reproduce:

1. Clone this repo: https://github.com/hearthsim/hearthsim-identity (git commit cf4e4060bab75dd59266c6fb4c125695479335b3)
2. Change tox.ini flake8 testenv dependency from flake8<3.4.0 to flake8==3.4.1
3. Run tox -e flake8.

flake8 will fail because of the files in */migrations/ which are excluded in the [flake8] section of tox.ini.

With flake8 3.3.0, everything works as expected.