These blisters are caused by pressure, a bit like the the end of the toe blisters and since you have four nerve endings at the end of each toe, they are so receptive to pain. Sadly these blisters can keep giving long after the initial blister has formed They can result in the loss your nail with damage to the nail bed , then the new nail can be damaged and misshapen, the remnants of the damage can still be seen a year later. 

How to help prevent these blisters

Routine nail care

if your toe nails are long or thicker than usual, then they need to be cut short or thinned down by a podiatrist to reduce the amount of pressure on that area. It is a simple solution that is often over looked. More information on self care for feet and nails.

Footwear

shoes, boots with more depth and are the correct length

Lace locking of the shoes and boots retains and secures the foot in the shoe, preventing excessive movement of the foot and creating pressure on the end of the toes from the shoe.

Toe props

these are custom silicone based and made to prop the toes from underneath and straighten them and reducing the pressure on the ends of the toes, they are made by a podiatrist.

Biomechanical assessment

with a prescription of orthotics or simple insoles- to establish the cause of the retracted toes or the hyper-extension (toe sticks up onto the top of the shoe) of the big toe, by a Podiatrist. Hoka oneone running shoes would be useful here as the same biomechanical issue is going on as getting blisters under the toe section. These would help to offload the pressure on the big toe joint (MPJ)

Running technique

be aware of how you run, especially downhill as this is the time when you are likely to develop these blisters, as the pressure at the end of the shoe can be huge and the repetition of impact can be relentless. Longer strides will make it worse, so adapting a shorter stride length going downhill would help a lot but like with any adaptation to your technique it will take time to change safely without incurring injuries. Talk to a running specialist or a physiotherapist on how to help you do this.