Hey John -
first things first, console.log won't work in Titanium - just replace with Ti.API.debug though :)
In running your code, i am able to see what your referring to - its an interesting issue. The separate contexts are created, as you'll note the lack of capacity to reference globally scoped variables from window to window. However, I'm not sure if the clock related functions are setup in their own context or not (possibly similarly to the UI thread). I've sent this internal to see if I can get some feedback.
In the mean time, what kind of blocking issue are you running into, my guess is that there is another way to accomplish what you are looking for?
Feel free to ping me direct, bertg_AT_grantges_DOT_com
Bert