Since the two cats are wary of each other, and she is already abit anxious - it is possible that the other cat has "claimed" all 3 boxes provided which is leaving her no other option but to pick her alternative place of preference..the kitchen. If possible, try keeping a litter box available for only her to use. This may take some time and patience and on a day that you are home. To start, place a clean litter box in a room that you can close off, away from the other cat - place her in the box several times in the day (when you sense she may need to go, or even when you don't). If she uses the box successfully, provide her with a treat, leave her urine in it for the time being, leave the door open now and allow the other cat to investigate. He/she may associate this box now with one that he/she cannot use going forward. Depending on the individual personality's of your cats - this may or may not work - but could be worth a try. Good luck.
In addition, if there have been any recent changes to the type or style of the litter itself - can also cause a cat to choose other alternative areas. A gradual introduction to a new litter is recommended. Ratio of 10:90 (new to old) to start.