GG Loader is only for converting maps ans entities over to AGK, it doesn't do any of the script work, the only scripts you will have are the basic default scripts that Preben has already converted, for custom scripts you will have to rewrite them yourself.
The creator of GG Loader comes on this forum quite a bit, his name here is Preben, he would be the best person to speak to about any issues you have with GG Loader.
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