JIRA treats all queries against NULL- or EMPTY-values as false. This is in line with most database systems.

However, negating such queries with NOT does not work, they remain false.

How to reproduce:

1. Create a minimal project MP
2. create two version V1, V2
3. create 3 datasets MP-1 to MP-3. All have the field fixVersion. Set the following state:
   • MP-1.fixVersion=V1
   • MP-2.fixVersino=V2
   • MP-3.fixVersion is EMPTY

Queries with expected answers

fixVersion = V1 ⇒ {MP-1}
fixVersion != V1 ⇒ {MP-2}
fixVersion IS EMPTY ⇒ {MP-3}
NOT (fixVersion = V1) ⇒ {MP-2,MP-3}
NOT (fixVersion != V1) ⇒ {MP-1,MP-3}
fixVersion IS NOT EMPTY ⇒ {MP-1,MP-2}

Actual results

fixVersion = V1 ⇒ {MP-1}
fixVersion != V1 ⇒ {MP-2}
fixVersion IS EMPTY ⇒ {MP-3}
NOT (fixVersion = V1) ⇒ {MP-2}
NOT (fixVersion != V1) ⇒ {MP-1}
fixVersion IS NOT EMPTY ⇒ {MP-1,MP-2}

This a) unexpected and b) requieres very ugly queries when you try to filter out subtasks of released issues.

References:
My Question on SO: http://stackoverflow.com/questions/28671796/jira-how-to-search-for-all-issues-that-do-not-contain-a-specific-value
My support request: JSP-221541