I looked at your query from a slightly different perspective. Not sure if this is going to be any better, but I'm joining to your transactions table 3 times instead of just once, based on the conditions specified. I'm not sure your conditions are correct, but you'll have to do any fixing of those specs. Here's my alternative, although it may not be any better:

SELECT r.dbPatID, p.dbPatFirstName, p.dbPatLastName, r.dbstatusdesc, r.dbAddDate, r.LastName, r.dbStaffLastName,

SUM(tc.LedgerAmount) AS Charges,

SUM(tp.LedgerAmount) AS Payments,

SUM(tr.LedgerAmount) * -1 AS Contracts

FROM vw_ReferralKPIs AS r

LEFT JOIN Transactions AS tc

ON r.dbPatID = tc.PatientID

AND r.ClientRef = tc.ClientRef

AND (

(tc.LedgerAmount > 0 AND tc.LedgerType NOT IN (1, 29, 30, 31))

OR

tc.LedgerType = 16

LEFT JOIN Transactions AS tp

ON r.dbPatID = tc.PatientID

AND r.ClientRef = tc.ClientRef

AND (

(tc.LedgerAmount < 0 AND tc.LedgerType NOT IN (1, 16, 45))

OR

tc.LedgerType IN (29, 30, 31)

LEFT JOIN Transactions AS tr

ON r.dbPatID = tc.PatientID

AND r.ClientRef = tc.ClientRef

AND tc.LedgerType IN (1, 46)

LEFT JOIN Patient AS p

ON p.dbPatID = r.dbPatID

AND r.ClientRef = p.ClientRef

WHERE r.dbAddDate >= '2014-01-01'

AND r.dbAddDate <= '2015-05-27 23:59'

--AND (r.dbStaffLastName IN ('') OR '' = '')

AND r.LastName IN ('Tio ')--OR 'Tio ' = '')

AND r.ClientRef = 'INV'

GROUP BY r.dbPatID, p.dbPatFirstName, p.dbPatLastName, r.dbstatusdesc, r.dbAddDate, r.LastName, r.dbStaffLastName

Note that I've eliminated one of the WHERE clause conditions because it's OR portion makes it irrelevant. I also took out the excess conditions which cannot evaluate to true. Let me know...