What kind of scripting are you adding inside? If you mean inline scripting (inside a tag, in an onclick attribute or something) then it should be fine. If you are adding code inside a <script> tag, then I’d recommend changing the slider initialization from
$(document).ready(...)
to
$(window).load(...)
or just moving it outside of the slider, if you can.
The problem usually occurs due to the contents of the first and last panel being cloned. Any scripting in these panels could then cause problems unless you use the new option “infiniteSlides” set to false; this option is available in the latest version.