Yes it will have required your input on what action to take for the infected file.
You could temporarily unplug your secondary monitor and see if that has any effect.
You didn't answer the question about a normal boot, on what monitor is the loading information, etc displayed ?
Is avast allowing you to boot normally without entering the boot-time scan ?
If not you can try a boot into safe mode,
http://www.pchell.com/support/safemode.shtml, avast doesn't start automatically in safe mode, trying to bypass the boot-time scan. There should be an avast Desktop Shortcut, double click that (once the memory scan is done) the Simple User Interface, Menu (right click on the skin), select Schedule Boot-Time scan.
The Schedule Boot-Time scan pop-up should allow you to set Advanced Options, primarily a default action, 'Move infected file to Chest,' there are options for possible system files and this is probably left at 'Ignore Delete or Move for System Files.' This should hopefully allow for the completion of the boot-time scan without user input required.