Sorry for the delay in getting back to this thread, but wanted to give you guys an update. If you were working with the beta of Articulate Storyline your logo won't appear in the published output for any logo added during the beta. The issue was we were storing all imported logos as SWFs, so we could only publish them as SWFs, so they won't appear in HTML5.
To fix this issue:
1. Go into Player Template
2. Delete the logo
3. Re-add it
Also, if you insert a logo as a SWF, that also will not appear in HTML5 because we don't support SWFs in the HTML5 output.
If that doesn't resolve the issue please log the issue with our support department so we can get your project file and investigate: