I found a strange behavior that I believe is a bug. I am using 2.0-alpha.9503 on OS 10.9.1.
First I redefined the keyboard shortcut for "Comment Line" in the system Preferences. This command is from the "Source" bundle and appears as alternative shortcut to the default ⌘/ in the bundle menu (I used ⌘- in order to avoid the rather clumsy command for german keyboard layout).
Right after that both shortcuts work fine. After closing and reopening TextMate, only the default shortcut ⌘/ works, the new shortcut is now ignored.
When I select Bundles -> Source -> Comments I can see that the commands are still set correctly. After that, both shortcuts work again, until I close TextMate and open it again: the new shortcut is ignored until the menu selecting Bundles -> Source -> Comments is opened up, after that it works till closing TextMate again.
I was struggling some time with this issue, without solution. Now after testing for writing this bug report, at least there is a simple workaround. But maybe it can be resolved. I also tried changing the Bundle "Source" itself, but that didn't do the trick either.