From the relationship view of a table both internal and InnoDB relationships are shown. When clicking the "Save" button, InnoDB relationships are dropped and re-created, even if no changes to them have been made. This is not generally a problem, but for those of us who work with tables with lots of data run into problems.
The relationship view should double-check to see if any changes have been made to the InnoDB relationships before starting to alter the tables.
Case-in-point: One of my tables has 121,000+ rows and is 850+Mb. Trying to set the "Choose field to display" option ultimately resulted in one of my two InnoDB relationships being dropped completely and not recreated (due to a timeout) and the "Choose field to display" not being saved.
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Moved to bugs.
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Fixed for 2.11.8, please confirm, here is the patch:
http://phpmyadmin.svn.sourceforge.net/viewvc/phpmyadmin/branches/QA_2_11/phpMyAdmin/tbl_relation.php?r1=10503&r2=11366&view=patch