I also have been having an extremely similar problem (started showing up around version 30 I think). My problem is that when closing the tab from in a chrome window it almost always still shows up in TO but as an inactive tab - but not 100% of the time. I have found that when closing the tab from within a tab but from another tab it very often (but again not 100% of the time) shows in TO as properly closed and not inactive. Also when closing it from TO very often it closes and shows as inactive (again not 100% of the time and almost all the time if the tab as already inactive). When the tab is closed but shows as inactive in TO instead of closed then the only way of opening it is using the chrome feature to reopen recently closed tabs - using TO to try to reopen it just takes you to the currently active chrome tab.
Also when closing it from TO very often it closes and shows as inactive (again not 100% of the time and almost all the time if the tab as already inactive).
When the tab is closed but shows as inactive in TO instead of closed then the only way of opening it is using the chrome feature to reopen recently closed tabs - using TO to try to reopen it just takes you to the currently active chrome tab.