Convert.ToDouble("4089.90") outputs 40.899,00 why?

You can set the culture for your thread with:

Thread.CurrentThread.CurrentCulture = 
       System.Globalization.CultureInfo.InvariantCulture;

You don't say where you are based, but the output is consistent with the current culture being one that has "." as the thousands separator and a decimal comma rather than a decimal point.

However, you state that the culture is the same - which contradicts this. Have you or the client changed (or customised) the "Standards and formats" on the Regional and Language Options? If the setting has been customised it will still read as "English (United Kingdom)" (or where ever) but will produce different results to the default.