When having 'noequalalways' set, invoking omnicompletion in top window causes the window height to be reduced, eventually causing below 1new to fail with E36: Not enough room error. This error is silenced, leading to all windows being destroyed with only E839: Completion function changed window message on the message stack. Also, both windows are deleted (probably because after 1new fail, completion operates on the wrong (non-temporary) buffer).
Test case:
:set noequalalways
:split
:resize 1
<C-x> <C-o> # on anything that loads files with 'below 1new'