If you've got a lot of books with this problem that points to a bug - if you open up a bug with a test case on the bug tracker we can dig into the cause.
https://bugs.launchpad.net/calibre
Bulk Conversion can be set globally by disabling heuristics/auto under text input in preferences (instead of book by book), but the whole point of having heuristics as the default is that otherwise text conversions don't come out very well.