It is called SARGability. When you add that where clause it causes a full scan. It has to evaluate every single row to determine if it belongs in the result set.
You could try splitting this logic into two pieces.
WHERE DEFAULT_STORE.[STORE ID] > ACTUAL_STORE.[STORE ID]
OR
DEFAULT_STORE.[STORE ID] < ACTUAL_STORE.[STORE ID]
Do a quick google search on SARGability and you will find lots of articles discussing what is happening with your query. Makes sense once you understand it.
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