Sorry Henrique. I missed your reply somehow. I was not commenting on you personally. I was commenting because this phrase "thank you for your comprehension" was used by one of our vendors in repeated emails. Our staff were getting a bit upset at the wording choice (the email contained additional instructions so it already sounded a bit condescending as a whole, and the comprehension was icing on the cake). Turns out they just used google translate.
Thank you for your comprehension.
Comprehension = capacity of the mind to perceive or grasp.
It calls ones intellect into question.
Thank you for your understanding.
Understanding = a state of cooperative or mutually tolerant relations between people:
By definition they can be very similar. By use, comprehension is either very formal or can sound very condescending.