Based on the SQL the only thing that quickly comes in mind is that no alias is defined for column userType. Could it be that both tables have this column so the SQL would be ambiguous. So perhaps something like:
SELECT
s.id,
s.groupId,
s.name,
s.managerId,
s.paymentType,
s.mustHave,
s.deleted
FROM
dealer_stores s
INNER JOIN
users u
ON
u.dealerStoreId = s.id
WHERE u.userType = 'Rep'
Also if you debug through the code, is that the exact statement that is used or is something appended to the SQL string.