Thought...
Have you numbered each tool ie, T1 is for roughing, T2 is for finishing. The post processor wouldn't recognise a tool change is required otherwise, it would use the same tool for both strategiesm and therefore not stop between roughing and finishing
First tool in g code line should read
T1 M6
Mach would then run the roughing programme
Then second tool in g code should read
T2 M6
It would then tool change and run the finishing programme
If your using Aspire to create the tool path, at the bottom of the tool database screen (where you select which tool your using) you'll see 'Tool Number' selection box with a drop down next to it.
Obv as mentioned above - select Tool 1 for roughing and Tool 2 for Finishing