I am not exactly sure whether you are using virtualization or not. In general, we fixed several issues related to MultiSelect widget (mostly related to virtualization) since Q1 2015 SP2 (version you are using).
That being said, would it be possible to upgrade to the latest internal build or check the next official release of Kendo UI due to the end of this week. If the problem still persists, I will ask you to send us a repro demo. Thus we will be able to further investigate the case and follow you up with more details.
Looking forward to hearing from you.
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