It has auto started for me but even with skinning turned off for Excel 2010 it has still rendered the grid lines invisible. I had turned it off when I upgraded from 2007 to 2010 because of this problem but with the prior version of WB telling it to ignore Excel fixed it. No longer. Ignore is also not working for cmd.exe.
I do not believe ignore has never worked on cmd.exe and never will do due to an oddity with that process.
If you continue to have problems with an app having excluded it I suspect the problem is not with WB itself but either the system colours or system fonts applied by the currently in use skin. These are global and excluding an application never has (and never will) exclude them from these.
I assume you are trying more than one skin as I could imagine the system colours in say the Metro skin potentially making the lines invisible.