Both Cave and Caroline adopted Chell when she was young. (Or, so I have found out)
And GLaDOS doesn't realise this. She shows hints of memory when she sais to Wheatley "What's wrong with being adopted?" after her joking about Chell being adopted in Portal 1. She probably vaugely remembered adopting someone, but had no idea it was Chell.
Also, you can see this portrait of Caroline and Cave and in the background of the photo.. in the shadows you can see a small girl. (probably Chell)
Also, there's the part with "Bring your daughter to work day" with Chell's potato experiment (signed by Chell) which further suggests her parents worked for the facility, and then further suggests her adopted mother is Caroline.
The fact that Chell would kill her own adopted mother seems strange. She clearly wouldn't have a hatred towards Caroline, becuase she's a very nice, caring person. Would Chell know that Caroline is GLaDOS by this point?
Did Chell know that GLaDOS was Caroline? Maybe Chell knew that Caroline died and had her life.. but.. she's still alive.. and killing.