What caused you vitamin d deficiency apart from the usual...

It may simply be that you aren't getting enough vit D even with supplements. The blood level only reflects the tissue level and if it is low, then the tissue level is also very likely to be very low. It's a bucket that needs to be filled up before it will spill over into your blood.

Despite your good diet you can be deficient - whatever you eat no more than about 10% of your vit D needs come from diet. In fact - if you are in the UK, or anywhere else in Europe, milk is actually not a good source of vit D:

"In the UK, cows' milk is generally not a good source of vitamin D because it isn't fortified, as it is in some other countries." (NHS fact sheet).

Almost all the stuff you find on the internet for vit D in milk applies to the USA where milk is fortified with vit D by law. That isn't done in Europe after a scandal where small children were poisoned by an accidental overdose of vit D at some point after WWII - it was fortified during the war. So you probably aren't getting as much as you think - vit D is found in oily fish, red meat and especially liver, eggs and margarine which is fortified even in the UK - but only to the same level as butter - and in fortified cereals! To get enough from diet you would need about 1/2lb of oily fish every day - or 17 eggs or a couple of pounds of mushrooms exposed to UV light. Not going to happen is it?

The main source is, as you know, skin production. However, in the northern hemisphere once you are north of about Turin in northern Italy or Minneapolis in the USA it becomes increasingly difficult to make enough. The sun's rays must strike the skin at above a certain angle and that can only happen in the UK between May and September and, even then, only between 11am and 3pm. Any sunscreen will reduce the amount made in the recommended 10 mins considerably: Factor 8 reduces the amount by over 90%. As we age this production falls away and by the time we are in our 60s it is a quarter of what it was at 20. Dark skin also reduces the amount made - including a suntan, a moderate suntan has a similar effect to Factor 12 sunscreen. I live in northern Italy - it is thought about 80% of our local population is vit D deficient and our local vit D guru, a medical doctor, tells us to take 2,000 IU/day throughout the winter. We're a long way south of London! Never mind Scotland...

Add all these factors together and it makes it increasingly difficult to top up a low level. If you are very deficient the usual supplements from the doctor are not enough, they are only about 800 IU/day. To replenish the level you require high dose vit D over several weeks. The usual approach is to give 60,000 IU/week for 8-10 weeks and then retest. It may bring the blood level up high enough so you can stop taking the high dose supplements but you still need to be retested a few months later - sometimes it falls a lot again and you need another course for a long lasting result. 

As for medical conditions - inflammatory bowel disease or malabsorption syndromes can lead to low vit D. Dietary vit D requires fat for transport into the cells - even for your supplements. Fat malabsorption is associated with a variety of medical conditions, including some forms of liver disease, cystic fibrosis, celiac disease, and Crohn's disease, as well as ulcerative colitis when the terminal ileum is inflamed. Obesity and gastric bypass surgery both also affect it. Obesity does it becaue vit D is a fat-soluble vitamin and the subcutaneous fat sequests the vit D and doesn't give it up to the other tissues.

A slight unkonwn is autoimmune disease. Low vit D is associated with many autoimmune disorders - but no-one knows whether it is cause or effect, ie does a low vit D level cause the autoimmune disorder or does the autoimmune disorder use up the vit D or cause it to be low for some other reason.

Does this answer your question - sorry it is longwinded but as you see there isn't a simple answer.