To reproduce the problem, make sure you have the latest versions of these packages installed:

devtools::install_github(c('rstudio/rmarkdown', 'yihui/knitr',
                           'rstudio/ggvis', 'rstudio/shinyapps'))

library(rmarkdown)
library(shinyapps)


render('test.Rmd')
browseURL('test.html')
# The gear icon looks ok


# Just need to start the deployment - don't need to wait for the whole thing
# to finish. You can stop it after it starts.
deployApp('testapp')


render('test.Rmd')
browseURL('test.html')
# The gear icon is messed up