I was working with the file api to upload files and for that I have disabled the plugins and found that multiple file selection is restricted in IE9. For selecting files plugins are they required? In chrome this is working and IE allowing to select single files.
I am able to replicate your issue at my end. Since you have disabled the plugins, the next option for the control is to use File Api for multiple selection and upload. The File Api module is supported in Chrome whereas it does not work in IE and hence you are unable to select multiple files in IE. You need either SilverLight or Flash to achieve your requirement in IE versions prior to IE10 (IE9 is an exception in this case that it has some compatibility issues with Flash module).