I had a similar situation with my counselor. His wife recently had a baby so he only came to school for part of the week then stayed at home the rest.
Admissions people know that it's hard to develop a relationship with a counselor the same way as a teacher so they will have that in mind when they're reading your recc letter. It'll help if you have a resume and/or bring a list of all the things you are involved in/ awards/ accomplishments. Also bring in a paragragh about you as a student. Whatever you bring in on paper will be what the counselor will have to refer to when she is writing the recc. So it's very important that you do this.
Here are some things you could do that can maybe help catch some alone time with your counselor:
a) Get a copy of her schedule. There should be one in her office somewhere or you can have the office print one out for you. There you can see all of the times she is available.
b) Come to school very early to catch her. If she is busy schedule an appointment to see her after school.
c) If she is still busy then I suggest asking your parents to call the school. Your counselor should be able to make time to see you, it's her job to do so.
If you do get a chance to meet with her make sure you have all important information handy. For ex. important deadlines, how she will send in her recc, how many schools you'll be applying for, etc.
Hope I helped