Hmm...seems to work fine for me. I use the basic colon formatting like this:

| Column 1 | Column 2   |
|---------:|:----------:|
| Foo      | Bar        |
| Foo      | Bar        |

I've assigned a hotkey to the "Format Table" menu option so, after making table changes, I press the hotkey, and the text table appears to be formatted properly. Are you doing something differently?