Doesn't seem to be the case for me.

Make a brand new character (by default 80 BP spent because HL defaults everything to 2).
Added Albinism BP spent 70/400

Added Ambidextrous BP spent 75/400

First post on Page 3. Search the thread to see if the bug is already reported before posting. :)

Magical Initiation

Page 50 of Street Magic shows the costs of initiation. When you select one (or both) of the options to reduce the Karma cost by 20%, the book specifically says "Round Up". Hero Lab is rounding down.

Now only 1 essence hole
 

The latest pdf of Augmentation does not have separate essence holes for cyberware & bioware (on page 128)

Chatty Quality not costing enough.
 

I've found that you haven't errata'd the Chatty Positive Quality.

It costs 10 BP instead of 5, as per the Unwired Errata. (Link leads to the Unwired Errata PDF on the Shadowrun website.)

I'm not sure what you are getting at. Are you saying Hero Lab isn't filling that Cyber/Bioware hole when you upgrade/replace?

Unless the essence holes specify whether they were bioware or cyberware holes, here's a situation that can result:

A character has 4 essence of bioware and 3 essence of cyber (halved, subtracting 1.5 from the essence attribute) = essence 0.5.

That character removes 2 essence worth of bioware, leaving 2 points of essence hole + 3 essence of cyber + 2 essence of bioware (halved, subtracting 1 from the essence attribute) = essence 0 = dead.

Oh, ok. I get it.

Did the older version of Augmentation treat the essence holes separately?

I think they've always been vague about essence holes - it doesn't say they are separated, it doesn't say they aren't separated.

Cyber/bioware both replace parts of the character's body. I think part of the reason they're being vague with it is that if a character loses some of these things, they can die of system shock as Mathais pointed out, Essence 0 being death.

I believe it was left vague with that in mind, but perhaps we should ask Catalyst this question?