I had this same problem, too. Make sure you cd to the directory where the app is located. Then type the app name or drag the app onto the Terminal window (the latter is what I did).
To be more specific, here's all of what happened to me. I made a directory named "boinc" in my home directory, then stuck the app inside. I hadn't cd'd to the directory, so the Terminal was still using the default prompt, which I believe is ~ (short for the home directory of the current user). I then had the problem you described. After trying several things without success, I noticed that boinc had created several files and a couple folders in my home directory. I suspected that it would work if I moved them to the boinc directory with the app, then cd'ed to the boinc directory and then tried to start the app, and sure enough it worked.
A side note: Afterward, in the Finder I got info on the boinc app and told it to open the app with Terminal. I made a shortcut to the app on my desktop. Interestingly enough, when I double-click the app it works -- it begins crunching without having to cd to the boinc directory. Maybe Terminal automatically defaults to the app's directory when a command-line app is double-clicked in the Finder. (Maybe not... I don't recall if I've tried running the app without switching to its directory *after* I got it working. I just set it up last night, after all. =)
Hopefully this will help you get yours working.
Now I just need to figure out how to get it to run only when idle. I changed the preferences to not run when the computer's in use and to wait for 3 minutes of idle time to begin, but it seems to ignore those preferences...