Hello all,
I've got an update on this problem. The issue wasn't the time stamps, though those may prove another issue once this is fixed. The problem I had was that the master_index file had reached its maximum size. I copied it over to make room for a new one, edited indexupdate.xml to include only 2012 and later index files, then ran:
ArchiveIndexTool -v 1 indexupdate.xml master_index &
This being the command that appears over and over in the ArchiveIndexTool.log file, but no master_index file appeared. The new master_index file was crated. I have yet to see if it will be continually updated as master_index is taking a while to build and I think the automatic update happens around 2 am, but I don't see why it wouldn't run as before.
Thanks everyone for the help, I'll ask if any other problems come up.
James