Hi Rocks,
You may have to 'Clean Library' from time to time.
If you change the directory name or filename, the next time you open XBMC it will scrape/take the new information but leave the old one.
So when you Clean the Library, it checks all the links and removes the ones that don't exist. So maybe that's why you're still seeing 'wrong' movies.
To do this, go into Settings, Video.
I use Media Companion too, but mostly for TV shows.
In regards to remote, do you have iphone/ipad or Android phone? There are a number of "app" remotes that use the touchscreen, and operate over Wi-fi.
Something like this? Has a USB dongle, works on 2.4Ghz band but really more a keyboard a touchpad than a true remote.
http://www.focalprice.com/HE275B/24GHz_M...Black.html
More information and price in the link.
Hope that helps, good luck.