Perhaps you are setting the background in a way aterm doesn't like. Check the "root command:" line of your styles file (usually in /usr/share/fluxbox/styles ; the individual files are named with the same names as the styles themselves, just look in the one for the style you are currently using).
Often, the styles use bsetbg or bsetroot to set the background. For whatever reason, these programs tend to not work well with transparency. I've found that Esetroot works well. I've only used Eterm though, so I can't say about aterm.
First check if you have Esetroot installed (just run it on a command line and see if it can find it), and if so, replace the root command line of your styles file with a command line that uses Esetroot, not bsetbg or bsetroot.