Hiya,
I hope your Border is feeling better today. I think your probably right, not particularly about seperation anxiety but I am quite sure anxiety will be playing a part. At two she is now pretty much and adult and will be more bonded to her people and more likely to miss them and she may be acting out of character due to this. Separation often gets harder for dogs as they get older.
Also given that they had a scuffle due to play getting out of hand and then having another spat she learned that she can take it out on the Boarder. I would think if she's getting worked up and frustrated behind a baby gate, when she comes out she is over excited frustrated and wound up and is taking it out on the Border.
Given that you have already tried the baby gate idea and that seems to be getting her more frustrated personally I would use the number they have given you, if it was me I would most definitely want to know. They may have someone else who they would rather she went to than a boarding kennel.
Have you tried giving her things to do whilst she is in the utility room like a stuffed kong, or some kind of activity (food related

) that will take her a while so that she has something to keep her occupied rather than getting worked up. When you let her out of the utility make sure that she is a on a lead. If it's just your Border that she's having a problem with can you not share times, have the lab behind the baby gate when your three are together and then let the lab in with the others for some mixing time and then have the Border in another room with you.
Goodluck.