Looking at it more, some files are getting skipped during load because the inode has been seen before, except in these cases the files are wrong:
scan: //<server>/<username>application_data/Sublime Text 2/Packages/Markdown has been seen before, skipping (using inode) previous path: //<server>/<username>/application_data/Sublime Text 2/Packages/DocBlockr inode: 18446735965056266256
On the latest load there were 14 skipped. This number and the files themselves vary.
I've set "ignore_inodes" to true in build 2200 but presumably that setting isn't read until after some other package files?