Darb's right, you should run the skimmer 24/7 except during maintenance.
During the break-in period (first 2 weeks) you'll probably had to adjust it several times...but it does sound like you've got airflow too high or the collection cup is too low.
Is this, in fact, a Red Sea Prizm skimmer?
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Former advisor and planted tank geek...life's moved on though.
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