Sorry, but your post is a bit on the confusing side. We likely need more information in order to determine what may be happening here.
WebHelp is kind of a "tripane" type of output. You have a main toolbar with buttons that open the TOC, Index, Search and Glossary. You have the pane on the left side that presents the TOC or whatever has been clicked. Then you have the Topic pane that presents the topic.
So I'm not sure what you mean when you say you "converted from tripane". Perhaps you can expound on that?
You also say that you "took all the necessary parts and put them into the right main body part, then used that as my start-up topic.".
That seems to suggest that you actually removed any TOC or Index or whatever and somehow managed to stick it into the single startup topic? If you somehow managed that, I'm not sure why you would then be surprised that the TOC and Index are now missing in the WebHelp.
As for empty contents or whatever, you are a couple of versions behind. You likely need to install patches to make WebHelp output properly understand our recent browsers. The best option is to upgrade to the newest RoboHelp. But if you can't do that for whatever reason, take a look at the link below:
Here is a sanitized screen shot of the tri-pane version before shifting everything into the content pane. Everything worked in IE and Firefox, it is just ugly with a tripane plus an added pane and menu bar.
Below the new single content pane with no search content. IE will give the TOC but no search. Firefox won't deliver either TOC or Search. Almost like maybe there is some active X block but all of my other projects work on both browsers.