Your issue is unrelated to the listed issue above.
The issue you mention is related to Script based workflows where the row you are selecting is the current live row returned from the underlying workflow. If the workflow hasn't completed execution, as far as it is concerned, you are selecting the correct row. This will only affect workflows which are slow at updating results to Alfred, most (especially non web based ones) should be instant.
Having said that, I have planned passing out the currently typed query throughout the workflow which may enable workflow developers to catch similar to what you describe (which may or may not be the desired behaviour).