user196: AFAIK, so far, BTC has been accepted in every Humble Bundle since they started accepting them… instead they weren't an available option with the Borderlands bundle.
Is there an official, semi-official, or educatedly speculated reason?
I asked but they didn't answer.
No "we can't read their mind" answer: if they didn't state the reason, I really don't see why anyone knowledgable enough couldn't make an educated guess.

user2306: Fraud.

Estrella (Humble Bundle) Jun 23, 15:46
Hi there,
Thanks for writing in to Humble Bundle Support!
Unfortunately, Bitcoin has been disabled for the Humble Borderlands
  Bundle. The individual payment options made available for a given
  bundle are determined when we finalize contracts with our development
  partners. In this case, it was 2K Games' wish to only support PayPal,
  and our native credit card processor, Stripe. I'm sorry for any
  disappointment this may cause.
In regards to the store, we've had to temporarily disable the Bitcoin
  payment option due to a sharp increase in fraudulent payments in that
  channel. While we do not have an ETA as to when the payment option
  will return, we are planning on bringing it back and we are working
  hard on getting things fixed as quickly as possible!
Again, I'm sorry for the inconvenience here. If you have any other
  questions or concerns, feel free to write us back!
-Estrella Humble Bundle http://support.humblebundle.com/

source

196: <p>AFAIK, so far, BTC has been accepted in every Humble Bundle since they started accepting them… instead they weren't an available option with the Borderlands bundle.</p>

<p>Is there an official, semi-official, or educatedly speculated reason?</p>

<p><a href="https://twitter.com/Lohoris/status/614548459606122497" rel="nofollow">I asked</a> but they didn't answer.</p>

<p><em>No "we can't read their mind" answer: if they didn't state the reason, I really don't see why anyone knowledgable enough couldn't make an educated guess.</em></p>
 2306: <p>Fraud.</p>

<blockquote>
  <p>Estrella (Humble Bundle) Jun 23, 15:46</p>
  
  <p>Hi there,</p>
  
  <p>Thanks for writing in to Humble Bundle Support!</p>
  
  <p>Unfortunately, Bitcoin has been disabled for the Humble Borderlands
  Bundle. The individual payment options made available for a given
  bundle are determined when we finalize contracts with our development
  partners. In this case, it was 2K Games' wish to only support PayPal,
  and our native credit card processor, Stripe. I'm sorry for any
  disappointment this may cause.</p>
  
  <p>In regards to the store, we've had to temporarily disable the Bitcoin
  payment option due to a sharp increase in fraudulent payments in that
  channel. While we do not have an ETA as to when the payment option
  will return, we are planning on bringing it back and we are working
  hard on getting things fixed as quickly as possible!</p>
  
  <p>Again, I'm sorry for the inconvenience here. If you have any other
  questions or concerns, feel free to write us back!</p>
  
  <p>-Estrella Humble Bundle <a href="http://support.humblebundle.com/" rel="nofollow">http://support.humblebundle.com/</a></p>
</blockquote>

<p><a href="https://np.reddit.com/r/Bitcoin/comments/3avl4z/humble_bundle_doesnt_accept_bitcoin_anymore/csgh84b" rel="nofollow">source</a></p>
