I bought a MSI Vega 56 and when I set the fan speed to let's say 50% on MSI Afterburner and check the fan speed on HWinfo it shows 60% it is always 10% higher on HWinfo and GPU-Z then what it is on afterburner so 90% speed on afterburner shows 100% on HWinfo. Also it happens when I use manual fan speed when I choose auto it shows the exact values on both softwares.
Use only one tool at a time to monitor any parameter. Check the value either in MSI AB, or the GPU-Z screen. Please also try doing a clean re-install of any overclocking too like MSI AB, as well as the GPU drivers.