Hello,

Please have a look at the screenshot at http://i.imgur.com/huNpI.jpg. Otherwise, the following text may not make sense.

A % character appears before every prompt then it is replaced by the prompt; so, it only flashes for a fraction of a second. However, if the buffer is empty when ZSH starts, such as when one has a ~/.hushlogin file, it results in the behaviour in the screenshot, which is % character followed by blank lines. 

Before you ask, the screenshot was taken via a new user account. There is no zshrc, zshenv, nor any combination thereof in the home directory. The ZSH versions tested are 4.3.9 and 4.3.10.

There is a global /etc/zshenv file that has the following contents:
# system-wide environment settings for zsh(1)
if [ -x /usr/libexec/path_helper ]; then
	eval `/usr/libexec/path_helper -s`
fi

The output of /usr/libexec/path_helper is the following:
PATH="/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/Users/sorin/.local/bin:/Users/sorin/.local/sbin"; export PATH;
MANPATH="/usr/share/man:/usr/local/share/man:/usr/X11/share/man:/Users/sorin/.local/share/man"; export MANPATH;

Thus, /etc/zshenv is not the problem. It could be a fault of Terminal.app, but it only happens with ZSH and no other shell.

Thank you,

Sorin Ionescu