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Are you using Mod Tool or a full version of XSI?
As far as I know MshEx doesn't support any data from Edit Flags, you'll have to hex edit the msh file to enable transparency after converting your dotxsi 6.0 text file with MshEx.

I'm using mod tool and exporting with MeshEx, which is more than likely the reason why edit flags didn't work.

But in any case, when I cleaned my map, my model fixed itself(I don't know why I didn't think to clean before ). Thank's for the help though .