I don't have experience on either Server Fault or Super User, but I believe your downvoted questions would be a poor fit for either:

 1. [Is there a web-based platform for publishing & editing FAQs?](http://serverfault.com/questions/494957/is-there-a-web-based-platform-for-publishing-editing-faqs) This is a product recommendation question, which is generally not accepted on SF or SU (or SO), and was closed as "Not a real question" (not as Off Topic). Contrary to your statement that the comments didn't indicate anything being wrong, a moderator commented on this fact.
 2. [How to choose a daemonized ed2k client](http://serverfault.com/questions/494564/how-to-choose-a-daemonized-ed2k-client). This is also a product recommendation question. There is one comment suggesting that it *might* be appropriate on Super User, but since product recommendations aren't considered constructive anywhere on the SE network, I'm don't think that comment spoke for everyone.

In other words, I think that your interpretation that your questions were closed and downvoted solely because users thought they would belong better on Super User was incorrect- I think they were downvoted and closed because they weren't appropriate for the SE network in general.