I'm a writer and not a keyboardist, so I prefer to produce my music as Sibelius scores and then play it back according to rules I set up in Kontakt.
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I use LASS 1.5, but my technique work with other sound sample libraries, as well. To address your issue, I take it that in Preferences of Sibelius you have checked, "Use Variant Sounds for Identical Instruments" and unchecked, "Use Same Slot for Similar Instruments." Another concern is the Soundset you are using. Typically I avoid auto-loading as, even under the best circumstances, it gives spurious results. If you are using Jonathan Loving's Soundsets, make sure to use the FIXED version of the House Style, because it does not auto-load. Finally, you should know that when loading a large number of samples (i.e an orchestra), Sibelius will start by assigning MIDI ports to the strings (#1 to Violins I, #2 to Violins II, etc.) and then will continue assigning MIDI ports next to the woodwinds, brass, and finally the percussion. Another way to approach the issue is think about putting one of the violins on a different Kontakt page (say, that which contains MIDI port 17-32).
Just a little about me. I get the same realism from Sibelius sheetmusic playback as others get by using a sequencer and a MIDI keyboard. These are links to the tutorials:
Getting string samples to sound realistic [url]https://www.youtube.com/playlist?list=PLbJ3UqfveVHX6BK1hlLnclKx6xcyRbIHW[/url]
Getting string samples to sound realistic - Two [url]https://www.youtube.com/playlist?list=PLbJ3UqfveVHWwvMyd0I-g3mRp58y00flA[/url]
I've used the playback techniques I've developed in my tutorial videos to re-record my violin sonata. The sound you hear at my Youtube channel, Novaclassica, is simply the raw sound samples as it issues from Kontakt, merely balanced off according to dynamics and given just a hint of convolution reverb to brighten it up. Here's the link to the violin sonata:
[url]https://www.youtube.com/watch?v=bKXwLj4B4oA[/url]
The next few videos to be released deal with string ensemble and divisi MIDI mock-up.