I think you got an issue with the tolerances in your features - in some of them you work with 0.01 and 0.5 angular.
Try to lower them to 0.001 and 0.1
But it works also in your part. Split the two extrude in the middle. Make the boolean substract for the first pair, the for the second and unite them after that and it should work. (I can't upload my partfile- an error occured...)
Perhaps it will be good to create an IR for this
If you change the length to a smaller value, e.g. LONGITUD = 1500mm, the subtract works as expected. I also suggest opening an IR with GTAC so that they can investigate.