Mr Smyth, 46, saw his long-term incentive pay-outs drop from £722,000 in 2012 to £646,000 in 2013, which pushed his total remuneration down from £1.31m to £1.2m, according to the group's annual report just lodged at Companies House.
His £326,227 salary is up to £336,316 in the current year, above the £319,587 paid to new finance director Paula Bell, one of the ruling triumvirate at the Edinburgh-based logistics group, which has no chief executive.
Her predecessor Paul Dollman received a total £760,000 (£1.73m). The third director, David McIntosh, whose retirement was announced in January after 25 years and who is working his 12 months' notice, received no bonus last year after the £61,000 in 2012. His total pay-out fell sharply from £848,000 to £608,000.
The remuneration report says there will be no pay in lieu of notice for Mr McIntosh, and he will not be made any incentive awards during the year while his 2013 awards will lapse in full. He will, however, retain his right to 2012 awards, subject to performance criteria, in "recognition of his contribution to the company".