Sorry this took so long to get back to you.
To answer your question. As far as "server setting" etc, it really depends on what exactly needs to be changed.
Is it displaying a code? Is there a number associated with the error? Have you been able to identify which pages are having the problem?
I would look at this systematically. Now you may not have the time to do so, considering that this is work and not always play; I completely understand if your idea of a fun Friday night isn't sitting in your basement analyzing which pages are not working with the Moz site audit.
Regardless, let's find out where the errors are.
- Can you run other Moz tools on the pages that are causing the error?
- Does the side audit display any error for those pages?
- Are you copy and pasting the entire URL into the tool?
Another thing to keep in mind is that Moz did take a hit from a few DDoS attacks so I know a few of the tools have been iffy on and on. http://health.moz.com/ is a great spot to check and see if the tool you are looking for isn't working.
I think every SEO Tool (Majestic, Raven, SEM Rush, Search Metrics) really are giving you the same data just packaged & interpreted differently. They all have a specialty of course and that being said I have my preferences. Majestic will dig for more backlinks, SEM Rush will give the best Ad data, but realistically everybody is fishing from the same pond, granted it's a big pond. With an unlimited budget I would have 3 different programs for different things.
The amount of data that these programs are trying to interpret is awesomely massive. I don't know if any SEO tool is spot on, even Google Analytics for example. I think of them all, as a guide.
I started with Search Metrics which was incredible expensive and way to in-depth for my knowledge of SEO and my projects.
Later transitioned to Raven which was great because they pulled data from Majestic and Moz, and gave some great step by step suggestions. The problem was their spider couldn't run most of the websites I needed.
Lastly I ended up on Moz. A name I remember back when it was SEOMoz. Sure there are issues, but I found not only were the tools pretty on target, but the community was INCREDIBLY helpful. Which is one of the main reasons I have stayed. And I am a N3wb in comparison to most of the guys on here!
I'm sorry you're having a bad experience with the tool!