Katie McPherson was 23 when she lost her life to DVT, a blood clot formed in a deep vein, after being sent home from two different hospitals in 2003.
The Scottish Public Services Ombudsman called for national guidance and a review of the way all boards manage DVT after an investigation. It said the different approaches used were a significant factor in her death.
However, last autumn Ms McPherson's father, Gordon McPherson, raised concerns that some boards were failing to follow the latest guidelines on screening after he received responses to requests made under freedom of information (FoI) legislation.
He wrote to Sir Harry about his findings and the Chief Medical Officer has given health boards until January 17 to confirm they are following the procedures set out three years ago.
In a letter, Sir Harry said the FoI requests indicated a lack of consistency among boards and he reminded them of the "responsibilty to fully implement" a guideline relating to the condition, known as Sign guideline 122.
Mr McPherson, from Langbank in Renfrewshire, said: "Why are guidelines produced at great cost in terms of the professionals who sit on the groups who write them if the guidelines are not used?"
One of his key concerns is that materials used by some health boards outlining how they check for DVT still use the term 'DVT excluded'.
After Ms McPherson's death boards were told to circulate patient advice leaflets which inform them doctors "can never fully exclude the possibility of a clot".
Ms McPherson, who was studying to be an occupational therapist, went to Edinburgh Royal Infirmary with a pain in her lower leg in January 20, 2003. After tests she was discharged with the advice there was "no thrombosis seen on this examination, therefore low probability of DVT" but was advised to see her GP. Her GP gave her painkillers the next day.
On January 22, she called the GP reporting no improvement and was told to go to the Royal Alexandra Hospital in Paisley, where doctors consulted her notes from Edinburgh which used the term "exclusion of DVT" and discharged her. Four days later she became seriously ill at home and died on the way to hospital.
Mr McPherson said: "It is a very long time ago, but it still feels like yesterday. Katie will never be forgotten."
While he was satisfied with the responses he received from a number of health boards, he said four - NHS Ayrshire and Arran, NHS Lanarkshire, NHS Highland and NHS Tayside - were all using the phrase 'DVT excluded' while NHS Dumfries and Galloway was working to old guidelines.
Sir Harry's letter to boards said: "Recent Freedom of Information (FoI) requests to NHS boards have indicated a lack of consistency in the implementation of elements of Sign 122. Progress update requests from the government in July 2012 also confirmed that implementation was still in progress within several boards. Some of the policies and procedures in place still seem to be based on Sign guideline 62.
"I am writing, therefore, to remind you of your responsibility to fully implement Sign 122 and to ensure that your Board is operating according to the best clinical and medical standards."
Mr McPherson said he was disappointed procedures were inconsistent but added: "I think Harry Burns is listening."
A Scottish Government spokesman said: "We are committed to raising awareness of the dangers of DVT and ensuring people with, or at risk of, developing these blood clots receive the best possible care.
"The ongoing implementation of Sign Guideline 122 has helped to identify adult patient groups at risk of DVT and ensure they receive appropriate treatment and care as required.
"Individual health boards have been working with the Scottish Patient Safety Programme to ensure it is fully implemented, and the Chief Medical Officer Sir Harry Burns has written to all health boards asking them to confirm that the guideline is fully implemented in their boards by January."