Two suggestions:
1) In the "Service" tab of the Topshim panel, there's a "calibrate" feature that you can use to get the system talking to the probe more effectively. Last year, we sent a probe out for service and when it came back we had a terrible time shimming it with Topshim. Once an engineer who happened to be onsite pointed out this button, we went through clicked it and let the software do its thing and we were then able to Topshim very effectively.
2) If you're primarily running organic samples, I've found we get better 3D shims by using an ASTM standard (40% dioxane in benzene-d6) and using the command "topshim astm 3D". We do this as part of our weekly maintenance with a doped ASTM standard, which also affords us easy access to quickly calibrating carbon 90-degree pw's.