WordPress – Receiving 500 internal server error installing WordPress on IIS 7 at GoDaddy

That errors means that you have a duplicate setting for UrlRoutingHandler. It's probably set in C:\sites\website1\ or applicationHost.config. You should be able to delete that line from the web.config file for \dd\web.config and you'll be set. To find the root cause, check the other config files in the tree (site level, applicationHost.config in this case) for UrlRoutingHandler.

It's unlikely to be that the .htaccess file is wrong. If it was wrong your site would not work at all instead of sporadically.

Is there anything in your Apache error logs? Assuming you're using Apache. Here's a link providing some info on finding your error logs although this will vary depending on how the server is set up. error log info

IIS presumably has an equivalent error reporting mechanism if you're running IIS although it's been a long time since I've used IIS so I'm not sure where it is.

Did you write the code running your site? If so and there's nothing in your error logs you'll probably need to add some error handling to at least tell you where the error is coming from.