This seems to be a regression of CONF-10775, for the "Search" use case.
"Search", which allows you to search for pages created in Confluence for linking, introduced since 2.9.x, loses Link Alias in both Rich-text and wiki-markup modes.

Steps to reproduce:

1. Highlight some text and click on the "Inser/Edit Link" icon
2. Notice the highlighted text being substituted in the "Alias" field on the "Link Properties" dialog
3. On the "Search" tab, enter a page tile in the text filed next to "Search" and click "Search"
4. Notice the reference to the "Alias" is lost (blank).

Note: The problem cannot be reproduced if the tabs have been changed (focus) when first opening the "Link Properties" page and then returning back to the "Search" tab.

Please review the attached flash video for more details.