1. She was destroyed in a Marvel Two-In-One story.
2. She was reassembled in the High Evolutionary 80s Annual crossover/event, only to die again, sacrificing herself to save the Avengers.
3. Madame Menace resurrected her again much later in an Iron Man story (and she sacrificed herself again).
4. She was then Tony's resident AI for a bit (and she sacrificed herself for him-- again).
5. A bit later, the AI was restored and put into the Iron Man suit. After a battle with Antigone, she wound up with Antigone's body (gold). She's been alive since this time.
Then suddenly she was back in her regular body for a cameo in "Disassembled."
There's nothing really very confusing about her though. She's Ultron's Bride of Frankenstein, who doesn't want to be.
But thanks for clearing that up. Characters who keep dying and coming back are usually my least favorite characters, so I don't really care about her that much.