Well, I found out that there is no way the Second Level cache can know if the database was changed outside Nhibernate/Cache, so what I did was creating a new column 'Timestamp' on all my tables.
On my queries, I first select the timestamp of the db using Session.Cachemode(CacheMode.Ignore) to get the timestamp of the db and I compare with the result from the cache. In the case the timestamps differ, I invalidate the cache for that query and run it again.
About the SysCache, even knowing it 'can work' on a WPF desktop app, I was not keen to use System.Web.Cache as my application would need the the complete .Net Framework instead of the Client Profile. I did a search and for my happiness someone wrote a Nhiberate cache proviver that implements (System.Runtime.Caching), witch is not a ASP.Net component. If anyone is interested you can find the source at: https://github.com/Leftyx/nhcontrib/tree/master/src/NHibernate.Caches/MemoryCache