Seems like maybe your arg1 is being defined before *command-line-args* gets a value. *command-line-args* is in clojure.core, so every namespace should be able to see it (unless you define a namespace and specifically tell it to exclude core or exclude that var). I don't know how Eclipse launches a REPL or how/when it loads namespaces or user code, so I don't know the problem.
But you could turn arg1 into a function, and then it should always return the current value of *command-line-args* (since it'll be resolved at runtime, and *command-line-args* should have a value by the time you call the function).
(defn arg1 [] (nth *command-line-args* 0))
Better, if (nth *command-line-args* 0) is really that much to type itself (which I don't think it is, really) you could write a better function:
(defn ARGV [n] (nth *command-line-args* n))
Then use (ARGV 0), (ARGV 1) etc. Keep in mind that vectors are themselves functions of their arguments, so you could just as easily do (*command-line-args* n) directly (once you're sure *command-line-args* is not nil; otherwise you'll get a NullPointerException.)
Using a lot of defs to assign names to things at the top-level is usually not idiomatic in Clojure. If you want to refer to command line arguments locally and just give them a shorter name for a while, there's let:
(defn foo []
(let [arg1 (nth *command-line-args* 0)]
...))
Again, this way arg1 should get its value at runtime (whenever you call foo) so it should work.