I updated my two primary machines (desktop and laptop) to 4.1 RC-1 from 4.0d SR-2, and I noticed that one started a full reindex and one did not. Both were current and matched all resources, I used both today.
I did a Resource compare to see if there was a difference, and the one that did not do a full reindex had older versions of 3 files - ELNT.lbxaud, excerpts.lbsexc, and LOGOS4HELP.logos4.