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how to convert output file to compatible format


I have submitted a mathematica job to unix system to run
where I use this command

bsub -q linux64 math < test7.m> out4

test7.m is the my input file, out4 is the output filename.

But The result generated though is what I want. But the format is different from what I typed ordinary. 

For examples,

     2           2
>      Sqrt[\[Gamma]  - \[Omega] ]                     

where this line happens to be in my result.
which is basically 

Sqrt[\[Gamma]^2 - \[Omega]^2] 

originally. Notice that especiall  ^2 of my superscript is off to the previous line from the term \gamma in the output file

If you all face this kind of problem can share with me? What I tried to do is basically sent my mathematica job to my school super computer to run. But the output is not in the user friendly format

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