In one file you are updating mat 1-5, in another you are updating 1-5 and 100-500, tho you don't have 100-500 defined.
Not sure if this will cause differences in the results, but it is an example of the differences in your input.
Why did you say they are the same?
Other differences that might also affect results including:
1. The precision format, for example, 2.8000000e+01 vs 28
2.The coordinate system.
In one file the second dof is the gravity direction.
In the other file the third dof is the gravity direction.
I know there is no difference for human understanding (if you've taken care of all the directions when you create the node, elements, loads),
but it might be different for the preprocessor or solver to understand.