New web applications created by PowerShell (e.g., manually or AutoSPInstaller in my case) or via Central Administration were not creating IIS sites on a small farm (2 WFE, 2 AS). While the web application and even the site collections were successfully created, the IIS site was not being created resulting in the infamous 404 IIS white page.

Here are the steps I used to troubleshoot:

1. Checked ULS logs: No issues found or recorded
2. Checked the Timer service: Timer Service was up and running on all servers, restarted anyway to be on safe side.
3. Restarted IIS on Central Administration App Server.
4. Checked Jobs and Job Definitions: Discovered one-time only jobs were not being executed. Tried to force run the one-time only jobs to no avail.
5. Checked Central Administration > Manage Services on the Server: “Microsoft Sharepoint Foundation Web Application” service was stopped on the app server. Restarted the service.

Now, all my IIS sites were populated and all the one-time only jobs successfully ran.