What’s your safety height set at? I only use Easel, but it says mine is set at .150". If your machine has a ridiculously large safety height, or the g-code is converting mm to inches and trying to lift 3 inches instead of 3mm (example only), that could be one issue.
Have you calibrated your Z axis? I don’t know how to do it in other programs, but I did a calibration video that shows how to do it in Easel (X-Carve Maintenance/Troubleshooting Videos - Add Your Own!), Z would be the same basic way, just use a way to measure height accurately and adjust the steps/mm or steps/in accordingly.