I figured out what was going wrong. Figure I'll share for posterity.
I found the following in the toolshed webapp log: "Not trusting file /galaxy-dist/database/community_files/000/repo_4/.hg/hgrc from untrusted user x, group x". Turns out this is usually caused when user invoking hg isn't the same user that owns the repo. Sure enough for some reason my startup script was running .run_toolshed.sh as a root. Fixed that and everything's working normally.
From: <Stewart>, Andrew Stewart <stewarta@si.edumailto:stewarta@si.edu> Date: Monday, October 21, 2013 11:55 PM To: "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: No "Upload files to repository" button
No "Upload files to repository" button after creating repository in self-hosted toolshed.
screenshot: http://imgur.com/AlQB1jL
Any ideas what could be wrong?