I'm running MAMP Pro v2.1.1 on OSX 10.8.5
I like to modify a couple settings for phpMyAdmin by modifying the settings in
/Library/Application Support/absolute/MAMP PRO/phpMyAdmin/config.inc.php
Actually I had the same issue... Pretty annoying but I found out after emailing them that the file at /Library/Application Support/absolute/MAMP PRO/phpMyAdmin/config.inc.php
is basically a temporary placeholder for your settings, inasmuch as whenever you start up MAMP the contents of the file at /Applications/MAMP/bin/phpMyAdmin/config.inc.php
is read and copied into it, overriding whatever's already there.
That said, here's what to do:
/Applications/MAMP/bin/phpMyAdmin/config.inc.php
The settings from the file you just edited should now be copied into the one that's actually read by MAMP and should take effect immediately.
For instance, I prefer to not enable the AJAX feature, so I did this:
/Applications/MAMP/bin/phpMyAdmin/config.inc.php
$cfg['AjaxEnable'] = false;
to the file... and all was well.