I suggest that you schedule a boot time scan. Right click the avast icon, select Start avast! Antivirus, Menu, ‘Schedule boot-time scan…’

– Most Delf Trojans add a Startup entry: Startup Entry Name, SysService - Process Name, SysService.exe
Use Task Manager to End the Process. Also to end the startup entry, Windows Start, Run, type 'msconfig without the quotes, in the new window select the Startup Tab, find the SysService entry and uncheck it.

If something is hiding files, then there is something else on your system, can you give an example of a file/folder that is hidden even after you change the hidden status ?

Also see Hidden things http://invisiblethings.org