...ran into an interesting issue.
Building an adept with some ware and lower beginning Magic Attribute..
First used the Point system (800 Karma) Purchased MA up to 4 (50 Karma). Added the ware (mostly Bio, 1.65 essence worth) and everything worked fine. If i attempted to go below 4 essence, it would not let me purchase the ware unless I went back and reduced the character's magic by 1 to 3. OK a nice little safeguard I thought..
Next I built the same test character using the standard Priority System with Magic at Priority D (2 MA) and Metatype at E (Human +1 Special Attribute Point) so I could get Resources at C (140,000). I applied the one Special Attribute point from Priority E to raise MA to 3 then spent 20 Karma to increase it to 4. After that I purchased the ware. However when I went back to the Common Tab to verify the augmented attributes, I noticed under the Build Summary the Special Attribute Points were listed as "-2 of 1", At first I thought "how can be" as I was supposed to have 2 MA from Priority D. Then it occurred to me the only other possibility could be that the programme was deducting the essence for the bioware from the characters MA rating of 4 which did not occur in the first test. Sure enough, when I removed one of the pieces of ware (Orthoskin 3) which moved the character above 5 essence, the Special Attribute point deficit was only -1 instead of -2. Doing so with the Point Build test character gave me no Karma back.
It doesn't make sense that this dynamic would be different between the two charagen systems.
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Update, the consensus I have come to after discussing the matter with others is that the Karma 800 option is handling the situation incorrectly. The augmentations I chose should have reduced the MA from 4 to 2. (which could be bought back up to 4 by juggling some Karma around)