There has been some issues with the workflows in earlier eZ publish version. There were some bugfixes to this in 3.2-6, I recommend you upgrade to this and see if it helps.
I am using a approval workflow. I have made a screen where the anonymous users submit their articles. Once, they submit, they are sent to approval of a verifier. After the verifier approves this article, they are published.
I have made all the articles to publish in a folder (name - "Resources") and made this as a section and assigned a usergroup "Verifiers" to approve these contents.
Under "Approvers" I have selected the "Verifiers" user group, under "Sections" I have selected "Resources", "users without approval" I have selected Administrators.
Whatever content I approve adds up to the queue and never gets published.
I am using 4.3.1 version of PHP and I will try by upgrading it to 4.3.6 and use CLI binary. Till now we were using CGI.
We had paid to include "Path Prefix" functionality. This feature will be available in 3.4 version only. So, we are waiting for this.