Android file system issues

I've been enjoying my new Nexus 7, my first Android device. I like having access to the file system but I am finding some weird issues. I use Astro File Manager on the device and file explorer on the desktop. Sometimes when if I move a file through Astro, it will not change locations in the file explorer, but if I move it using file explorer, it shows up fine in Astro. This lead to files being in different locations depending on where you look. This makes managing my files quite frustrating.

Any advice? Is there a way to make sure I move files around without running into this issue?