Excessive Custom Scan time

I've recently noticed that my Custom Scan ("Full System Scan") is now taking an excessive amount of time to complete.  I use a wake up mechanism to wake my laptop at a specific time to start the scan on a weekly basis.  The wake up software keeps my laptop up for 3 hours and then hibernates.  This used to be sufficient to complete the scan.  The scan now takes 18+ hours to scan 1,428,248 items.  Any ideas what could be causing the excessive scan time?