I know this is officially closed, but I am running Alfred 2.1(218) and Maverick (10.9 official release) and am experiencing problems with Spotlight and Alfred not indexing entire volumes.
I have a 6.2 Macbook Pro with two internal hard drives (the primary SSD is indexed, but not the secondary HDD). I have rebuilt the the spotlight cache and ran the "manual method" of reindexing volumes multiple times.
I'm sharing to see if I am the only one experiencing this issue.