Got trouble getting everything working?

Here are the most common pitfalls.

First of all:
If something doesn't work as expected after an update, please try restarting your iPad.
I haven't tracked down why yet, but sometimes this helps.

Trouble to connect

Well, first of all check your XBMC server setup.
In 9 out of 10 cases, it's Windows firewall blocking the communication between XBMC and the remote.
Please make sure that the port that's entered in XBMCs networking setup is allowed, as well as port 9777 UDP (for gestures).
You can verify wether your iPad is able to connect to XBMC by opening safari and browsing to http://xbmcIP:xbmcPort (replace xbmcIP and xbmcPort accordingly). You should see XBMCs web interface. If you don't, something is wrong with either your network or XBMC settings.

Aside from windows firewall blocking communication, a common pitfall is another program using the same port as XBMC. Port 8080 for example is commonly used by sabnzbd+, a news bin downloader.
In this case, changing the port in both XBMC (Settings->Network->Services->Port) and XBMC Commander to something different like 9393.

Gestures not working

First of all, double check that "allow programs on other systems to control xbmc" is enabled in XBMCs network settings.
If you're running XBMC on an aTV: Go to the ipads system settings app and toggle the "atv workaround".
Gestures are transmitted on port 9777 UDP. Make sure this one is allowed in your firewall.
I've heard from various sources that a router restart sometimes solved this problem too, so you might want to try to reset your WLAN router.
If everything fails, the aTV workaround should work for other systems too, so please give that one a shot.

TV show banners / posters not showing correctly

XBMC Commander can't influence what kind of tv show thumbnails it gets. That's set up in XBMC.
But sometimes the apps built-in autodetection gets it wrong. in this case you'll have to open the ipads system settings app, and select the appropriate thumbnail type for your tv shows by hand.
If you want to move from banners to posters, you'll have to change your scrapers settings, and rescrape your library.
Note: There are plans to change this behavior thus allowing xbmc to handle posters and banners side by side. So we'll see this in a future version of xbmc, at which point i'll add the free choice to the app as well.

Empty movie / tv show / music library

In order to get the most out of XBMC Commander (and out of XBMC!) you will have to set up your media sources, set a content type for each of your source, and turn on library mode.
I won't go through this here. If you haven't done this before please follow the XBMC Quick Start Guide.
Just remember to set the content for each source.

Network shares in file mode are empty

If you're using password protected network shares as sources, you might need to move your username / Password credentials from sources.xml to passwords.xml.
To do this, locate your userdata folder on your XBMC machine. In sources.xml, remove the "user:pass@" part from your network shares.
Then create a passwords.xml with the following:
<from pathversion="1">smb://SERVER/</from>
<to pathversion="1">smb://USER:PASSWORD@SERVER/</to>
This should remove the issue (and make your XBMC installation a little more secure btw)