Well, I am not sure what the cause is, but I did find a work around. I modified the post processor and add the command:
G00 X0.0000 Y0.0000 Z2.0000
immediately after the G43, "Set tool length" command (Inserted between lines 440 & 450), the soft warning disappears. I can only assume that because the Z is sitting outside the limits when the tool change is requested, and even though the SET TOOL LENGTH OFFSET command puts it back within limits, unless the next command requests a Z move, I will receive a soft limit warning.