You are using a very old version so variations in how the help works in different browsers do not surprise. Indeed, it is highly likely it will not work to an acceptable level in some browsers.
You say you are using WebHelp Pro. Does the server have RoboHelp Server installed? If not, you should be generating WebHelp (not WebHelp Pro).
See www.grainge.org for RoboHelp and Authoring information
We have RH server installed, but we also publish as webhelp for those employees that do not have access to our intranet where we house our project.
In addition to what Peter mentions, you would want to make sure you have installed all the latest updates for both RoboHelp 9 and whatever version of RoboHelp Server (especially the update link shown below.)
- Adobe - Support : RoboHelp Support Center : Service Releases
- RoboHelp Server Update 9.0.1 is here ! – TechComm Central by Adobe
Adobe Certified RoboHelp and Captivate Instructor