I've occasionally felt the same way, and it certainly wouldn't be the first time it came up on these forums. But I can't really come up with a working theory besides humans having a terrible perception bias.
By all analysis, the shuffling RNG is fair in its implementation, and works properly when the game uses it. Though, I sometimes wonder if there are situations where the game inadvertently does a "Shuffle Under Top" (like after a successful Augury), when the rules should dictate a "Shuffle Everything" kind of shuffle.
I'm just guessing, but the problem (if there is a problem) is likely not so much a matter of randomness, it is that the game appears to have different shuffles for different situations, and possibly a card bug or UI glitch is affecting the implementation.
Edited by Ethics Gradient, 11 May 2017 - 01:23 PM.