I will definitely submit a problem report, since it seems we've confirmed a problem/bug and not operator error.  Thanks.

I just tried this and I am getting expected behavior with no bugs. Each take is going into its own lane. So whatever the issue is seems to not be a universal bug. I wonder if there is some setting in your aud.ini file that's causing strange behavior. I had a situation where an old key binding from way back (perhaps Pro Audio) was creating a "bug" in X3 behavior. You could try wiping out and recreating your aud.ini file.

Hi Dave,
 
I have confirmed the issue and reported it to development. The problem occurs if you have "Store Takes in Separate Tracks" enabled for loop recording. If you close and reopen the takes after record the GUI refreshes properly however, the comping behavior of muting previous takes is not working under this setting.
 
In general I don't recommend this setting, particularly with audio as it can add up quickly. These settings pertains to loop recording, not take recording in general so it's not necessary for this scenario. In the meantime, please apply the setting of "store takes in a single track" to avoid this issue.
 
Let me know if you have any questions.
 
 

Thanks for working on this.  I can definitely adjust the setting as it wasn't set that way for any particular reason (i.e. I had to pick one or the other).
 
If I have more problems/questions, I will post here.

Thanks, Dan!