This isn't much (or any?) of an issue when HistoryURL provider exists.  That said:

Repro steps:
1. For an intranet web site that you've visited frequently (typed visits), say "cr".
2. Open chrome://omnibox
3. Check the boxes "show all details" and "show results per provider".
4. Type "cr" in the box on the page.  Hit "submit".
6. Observe in the "Results for individual providers" section for HistoryQuick, the line for http://cr/ has a fill_into_edit of "cr/" and an inline autocompletion of "/".  This is all reasonable.  (The omnibox adds trailing slashes to known intranet hostnames to make it clear these are URLs.)
7. Now revise the box to contain "cr/" and hit submit.

Expected results:
8.  In the "Results for individual providers" section for HistoryQuick, the line for http://cr/ has a fill_into_edit of "cr/" and an empty inline autocompletion.

Actual results:
8.  The line for http://cr/ has a fill_into_edit of "cr/" and an inline autocompletion of "/".  In other words, if this suggestion actually appeared in the omnibox, it would show "cr//", which the second slash being the selected inline autocompletion.

This is particularly problematic because if the user wants to delete and type something else, they cannot easily.  Press backspace will delete the "/" inline autocompletion, returning the input text to "cr/", which then immediately gets re-completed to "cr//".  It's impossible to backspace out of this state.