Install was quite easy but now my home link in main menu is acting erraticaly. Every now and then, the usual site home link is replaced with aliases, other sites name from the server, home link with the mail. prefix , or, even worse, site links with https instead of http. To stop that, I have to put the Joomsef off for a while then flush the caches then put Joomsef back on. It's then normal for a few hours and it starts all over again until I redo the flushing procedure. The worst now is the fact that all search engines have indexed the bad home page link and tonnes of wrong url of my site and I've got more and more 404 :(
I must say that I spend hours changing all configuration setting that could impact on that to no avail. I deeply frustrated with the product and if I don't find a solution urgently I will give it up.
I think that the problem in your case will be most likely neither in configuration or JoomSEF, but in incorectly created links within your site.
JoomSEF will translate the links it detects. If you have wrong link created within site, it will result in wrong (or duplicate) SEF URL.