Strange, it works for me, but try this:
(setvar "cmdecho" 1)
(command "_.-etransmit" "_c" (strcat (getvar 'dwgprefix)(vl-filename-base (getvar 'dwgname))".zip"))
You can at least see what is happening with the command prompt this way (press F2 if you don't see everything), perhaps it will make it more apparent what is happening.