I just noticed this same problem.
The current M6 macro does not update the tool number. You need to add it to your macro, so it updates to the current tool. The M6 macro is located in macros folder inside of the profile folder you are using.
Exit Mach4.
Filename is M6.mcs
Just add this line
mc.mcToolSetCurrent(inst, selectedtool)
after or before this line
wx.wxMessageBox('Toolchange finished')
Save the M6.mcs file, then start Mach4. Wallah!