phpMyAdmin

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check whether your config file is used at all, add a line:

die( __FILE__ . ' : user config.inc.php opened for read');

maybe related to this bug :
http://sourceforge.net/tracker/index.php?func=detail&aid=1959855&group_id=23067&atid=377408
- if no config file is found fontsize is not changabe.

It's had something to do with the config.inc.php file. I finially started
with a very short config.inc.php file (no comment line or anything but
this) of:
$i = 0;
$i++;
$cfg['Servers'][$i]['auth_type'] = 'config';
$cfg['Servers'][$i]['user'] = 'root';
$cfg['Servers'][$i]['password'] = '';
$cfg['Servers'][$i]['host'] = 'localhost';
$cfg['Servers'][$i]['connect_type'] = 'tcp';
$cfg['Servers'][$i]['compress'] = false;
$cfg['Servers'][$i]['extension'] = 'mysql';

Now it's working. The hardened php on all 3 servers must have something to
do with it not liking the config sample file :( Strange I hadn't had a
problem with it until 5.1. Anywho, I guess this is now a non issue.

Must be your system. I installed pma2.11.6 (7z,englich) today: no problem
changing fontsize.
Same on http://pma.cihar.com/STABLE/ . I tried various browsers (IE6,
Opera 9.27, Seamonkey 1.1.9 all on w2k). I can't reproduce the issue.

Forgot to say the file in question is libraries/common.inc.php

I have to verify this problem have done the following:
Tested with virgin installs of 2.11.4, 2.11.5, 2.11.5.1, 2.11.5.2, and
2.11.6 to ensure no upgrade issue is present. I have also installed each
into it's own sub-domain (yes, I made 60 sub-domains) to ensure no cookie
issue or cross contamination is present. I have done these tests on 3
different servers to ensure server related issue are not present. I have
tested in both Internet Exploder and FireFox to ensure it isn't browser
related. Results are simple:
2.11.4 = Uses font size
2.11.5 = Uses font size
2.11.5.1 = Ignores font size
2.11.5.2 = Ignores font size
2.11.6 = Ignores font size

I tested every package (of the stated versions) with the same result. I
compared every package of each version stated and found no difference in
the packages per version. Therefore package has nothing to do with it
working or not working. I have tried each version and package with and
without the "./config.inc.php" file present which had no effect other then
knowing that the file is not even found when it is present.

Thank you for your time;
Bob Marion
http://www.nukescripts.net

still have the problem here with phpMyAdmin-2.11.6-all-languages.tar.bz2.
can't change fontsize...

same problem with phpMyAdmin-2.11.5.2-all-languages.tar.bz2
font size settings are not working.

hmm, works for me in phpMyAdmin-2.11.5.2-english.7z (FF2)