If you are just using the G41/42 (without the P?.?), I think you need to have a tool change (M06 T??) in your program prior to the G41/42. Without that, the software doesn't know what tool table entry to use.
I just did some playing and found the following:
G41/42 without the P?.? parameter and no active tool (Tool 0) - It appears that the entry for Tool 1 in the tool table is used.
G41/42 without the P?.? parameter and preceded with a tool change (M06 Txx) - The tool table entry for Tool xx is used.