Alright, I took a close look of the source code, and it seems that the program treats a stimulus of all zero as something wrong in the input from the user, thus disallowing any glt analysis.
My suggestion is that you consider running 3dDeconvolve with this stimulus as usual for this subject's data instead one of all zeros for two reasons: (1) If you feed in all zeros for this stimulus, 3dDeconvolve would assume that those moments as resting state and would use the data points for baseline estimation, which is not what you want. (2) With a usual stimulus file without zeroing anything, you could keep everything consistent, and still run all the glt analyses as usual. Since you are doing deconvolution, the worst part is that you would not want to look at the results of the impulse response function of this stimulus and any glt tests that involve this stimulus.
Gang