Okay, I’ll give you that we really don’t know what happened to Angel’s mom. However, Jack’s justification for locking up Angel in a box is for “what she did to her mother.” So, according to Jack, Angel did something to her mom, and then Jack put Angel onto her new throne inside her little box as a consequence. He says this just before the BL2 Vault Hunters reach the Information Stockade.
Now in that side mission, Get to Know Jack, there are two specific ECHOs that should be considered when Jack does say this to the Vault Hunters. One is when we learn of Jack putting a very young Angel into a possible early version of Control Core Angel, with Angel pleading to see her mom, but Jack replies that “She’s not coming back.”
The second ECHO is the one you cited above, where one of the techs mentions Jack’s wife (presumingly also Angel’s mom). At this point, Jack has already gained significant influence and power within Hyperion, to the point that he has VP Jeffrey Blake answering to him and that he already has the (Control Core) Angel project in progress, if not necessarily completed.
We now take these three separate accounts and find that they are not consistent with each other. You can take any two, and there wouldn’t be a discrepancy. But once the third account is considered, there is an inconsistency in the order of events.
Now, if we take the two ECHOs at face value, then that leaves Jack’s own words into question. We don’t know if Angel ever did anything to her mom. HOWEVER, Jack did not put Angel into a box using whatever Angel did to her mother as the justification. He uses this lie to illicit some sort of false sympathy and justification for his actions once the Vault Hunters learn of Angel’s ordeal.
Later on, it seems that Angel’s mother has tried to do something about the “Angel” project (though we can assume she wanted to free her daughter from Jack’s machinations, there is no evidence to support that was her intent, or even if Angel’s mother knew that Angel was at the center of the Control Core Angel. Then she disappears. Jack doesn’t talk about it. He doesn’t want anyone to mention it. That is a red-button issue for him, so much so that he will go on tilt if his wife is ever mentioned or referenced. Knowing Jack’s propensity for lying and scheming, we could safely assume that he was probably lying about Angel’s mother as well. At the very least, Angel’s mother seems to represent something that Jack wants to keep buried and forgotten. It may not necessarily have anything to do with Angel herself, but I think it’ a pretty good bet that it is.