This occurs when you have installed a web application using our applications installer while PHP is set to Apache Module mode.
Your application was installed correctly using your user account, but when the application goes to upload files it is doing so as the 'apache' user rather than as you, which creates the mismatch in permissions.
To remedy this, change the PHP mode to FastCGI under Web Hosting Settings for the domain in your hosting account. This will mean all files uploaded in the future will be done using your user account and not the 'apache' account.
Exact steps to do this can be found here.
If this does not resolve your problem, please open a support ticket so we can investigate further.
