Vimium disables/breaks `confirm` and `alert` on all pages

I recently noticed that various pages weren't working for me as they should. I eventually tracked this down to window.confirm always returning false.

Steps to reproduce

1. Create a new Chrome browser profile
2. Install Vimium
3. Open any web page and pop open the developer console
4. Execute confirm("check confirm?");
5. Execute alert("hello world!");

Expected behaviour

Steps 4. and 5. should both result in browser popups. confirm should return true or false depending on whether the user clicks 'OK' or 'Cancel' on the popup.

Observed behaviour

confirm(...) returns false immediately, without displaying a popup. alert similarly returns immediately, without displaying a popup.

Disabling Vimium doesn't immediately fix the issue, but a subsequent browser restart will. Reenabling Vimium causes the issue to recur.

Version details

Mac OS X 10.11.3 (15D21)
Chrome 51.0.2693.2 dev
Vimium 1.54

No source file or test is named. Reproduce the issue using the listed Chrome and Vimium versions, including a browser restart, then trace how Vimium affects page-level alert and confirm calls. Done when both dialogs work normally with Vimium enabled and confirm returns the user's choice.