It seems Isha upanishad is available in Kanva and Madhyandhina recensions. These two appear to be two shakas. How can same upanishad be available in two shakas? Which version is generally used while commenting?
To the question "How can same upanishad be available in two shakas?" ,
There is no prohibition for a certain Vedic passage or verse, whether classified as Upanisad or not, to be part of different recensions. Vedic recensions are natural evolutions (or side effects) of oral (and aural) tradition by which the concepts were passed on through generations. From that angle if we see, it is perfectly understandable that two recensions adopted the same text or passage or set of verses, whether they are part of Upanisads or not.
An example is Rudram - though it is called Rudropanisat, it is part of the Karma Khanda. The Rudram is part of multiple recensions of Yajur Veda. Of course it is not in the same classification as the Isavasyam in your question, but it is a simple example to show that a set of verses can be part of multiple Sakhas. The same applies for Upanisads as well. This is contrary to the belief by some people that a given Upanisad should belong to only one Sakha. Though this kind of classification holds true for many major Upanisads, this is not necessarily a written (or agreed upon) rule that binds all the Upanisads.
As for the reason why & how Isavasyam ended up in two Sakhas, Swami Vishwananda provided a nice and crisp answer.
Which one is used for commenting - I have seen the commentary only for the version in Madhyandhina Sakha. Other commentaries may exist, or might have existed in the past.
Hope this helps.