It's difficult to say but some reasons might be:
-If you are running a number of other applications at the same time this can cause a bottle neck for your computer.
-Make sure you're running the latest version of the Studio One software. This guide will show you how to download the latest version -- http://support.presonus.com/entries/21879320--2-Software-Install
-Your hard drive. If you are using a 5400 RPM HDD (as opposed to a 7200 RPM HDD or a solid state drive) then you may experiences periodic hiccups in performance, pops/clicks, drop outs, etc. 7200 RPM is industry standard for digital audio recording.
-Your processor. Make sure your processor meets at least the minimum spec for your gear; however a processor that only meets the bare minimum will also experience periodic issues depending on the workload being put on it. Core 2 Duo is minimum, an i3+ is recommended.
-Your RAM. Make sure your installed memory meets spec. 4GB is the bare minimum for Studio One and essentially all of the PreSonus recording interfaces. Having at least 8GB is recommended.