The chkdsk /r is the normal cure for unmountable disk/drive errors and it seems to have solved that.
What applications failed to start? Did you do as suggested...and try uninstalling/reinstalling?
From what I see...any application dependent on Visual Basic or MS.NET may reflect such errors.
Take a look in Event Viewer and see what errors are noted...which may assert references to Side By Side or ID #32 or ID #59. Double-click such and post the detail.
How To Use Event Viewer - http://www.bleepingcomputer.com/forums/t/40108/how-to-use-event-viewer/
It would probably simpler to uninstall/reinstall the applications where you experience these errors...contrary to what you state, this error message seems to only occur in specific applications.