As far as the ability to locate an item in the left list is concerned (scanability indeed tends to become quite an issue in long lists), alphabetic order does make sense from a UX point of view.
That being said, you might want to
- ask your colleagues why they prefer a different order
- ask your colleagues what that different order would look like
- spend some time thinking about what order would suit the users best
- if 5 items out of a list of several hundred turned out to be getting selected in 90% of all cases, that would be a perfectly fine reason to move them to the top (separated from the alphabetically sorted rest by a divider element)
- if possible, ask your users what kind of sorting they would prefer and why.
Sheesh, you've been asking about the right hand side box, right?
Assuming that the left pane is sorted alphabetically, keeping the same order on the right hand side would be helping consistence.
Ultimately, the question it all boils down to is: would the order of selected items be important to the user and/or the further workflow?
Asking your colleagues/users about the rationale behind their preference won't hurt in any case.