(ok 3.1.2) Can't NULL a column with a relation defined

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Moved to support. At step 4 you are defining a relation, but
to do this, I think you defined a primary key on c2. While
doing this, MySQL removed the NULL attribute because "a
primary key column cannot be NULL".
http://dev.mysql.com/doc/mysql/en/alter-table.html

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I insist it is a bug. Why can I do the same thing manually,
through UPDATE `t2` SET `c2` = NULL, but not through that
checkbox?

And it's perfectly legal data structure. Let me show you:

`category`
--------------------------------
id | desc
-----------------------------------
1 | Liquid
2 | Fruit
--------------------------------

`items`
--------------------------------
id | desc | category |
-----------------------------------
1 | Water | 1
2 | Orange | 2
3 | Apple | 2
4 | Cat | NULL // Category
unknown and/or not yet assigned
--------------------------------

So in my example:
1) `items`.`category` has a foreign key relationship to
`category`'.`id`;
2) `items`.`category` is set to NULLable (and perfectly
holds NULLs if I add them manually).

AFAIK that's so-called 'weak' foreign key relatioship.

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Oh, I thought you were talking about the structure of c2
losing its NULL. Which MySQL and phpMyAdmin versions are you
using?

Please add to this tracker the export of structure and data
for your 2 test tables, ensure you use "add into comments
relations".

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CREATE TABLE `purchase_grouping` (
`group` int(10) unsigned NOT NULL auto_increment,
`refer` int(11) unsigned default NULL,
PRIMARY KEY (`group`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_bin;

--
-- RELATIONS FOR TABLE `purchase_grouping`:
-- `refer`
-- `transactions` -> `id`
--

CREATE TABLE `transactions` (
`id` int(11) unsigned NOT NULL auto_increment,
`post_date` date default NULL,
`amount` decimal(8,2) NOT NULL default '0.00',
`refer_tran` int(11) unsigned default NULL,
`refer_purchase` int(11) unsigned default NULL,
PRIMARY KEY (`id`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_bin;

--
-- RELATIONS FOR TABLE `transactions`:
-- `refer_purchase`
-- `purchase_grouping` -> `group`
-- `refer_tran`
-- `transactions` -> `id`
--

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With phpMyAdmin 2.6.3-pl1, under Firefox 1.0.6 with
Javascript enabled, when editing a row for the
purchase_grouping or the transactions table, I have no
problem checking the Null box: this saves a NULL value in
the corresponding field.
For example, this query is generated:
UPDATE `purchase_grouping` SET `refer` = NULL WHERE `group`
=1234 LIMIT 1 ;

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phpMyAdmin 2.6.3-pl1, Mozilla 1.7.11, JS enabled, JS
console doesnt show any errors.

1) 'Browse' Purchase_grouping' table.
2) Click to edit a yet unreferred item (in my case id = 4);
3) Change 'refer' column to some value that exists in the
related table, say 3708.
4) Click GO.
5) Displayed:
--------------------------------------------------------------------------------------
Affected rows: 1
SQL query:
UPDATE `purchase_grouping` SET `refer` = '3708' WHERE
`group` =4 LIMIT 1 ;
--------------------------------------------------------------------------------------
6) Click on the same item again to edit it.
7) Check 'NULL' checxbox and click GO
8) Displayed:
--------------------------------------------------------------------------------------
No change
--------------------------------------------------------------------------------------

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phpMyAdmin 2.6.4-pl1, Firefox 1.0.7, JS enabled. I do
exactly your test.

After step 7, I get:
UPDATE `purchase_grouping` SET `refer` = NULL WHERE `group`
=4 LIMIT 1 ;

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I guess we won't get anywhere this way, would you please
email me privately -- w-e-s-h-a (-at-) h-o-t-m-a-i-l.c-o-m
so I can arrange direct shell access for you to the system
in subject?

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P.S. I guess it's something about multiple relations and/or
data set size. When I try it on the actual database (6
tables, ~~5000 records), it fails as described in the bug.
When I export and reimport it under a different name through
phpMyAdmin, it also fails. When I try to cut it down to a
more reasonable size (3 tables, 10 records), it starts
working properly.

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Moved to support. Emailed privately, waiting for answer.

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No reply from user -> closed.

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Sorry about the delay, at the moment I'm busy with other
things, but I still experience this problem. Let's just
give it the lowest priority possible for now, but not close,
please?

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Still no reply.

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Okay, I found how exactly ro reproduce it.

Correction to step 3: Insert MANY records in t1, enough so
the relationship field will be displayed as "TEXT field +
LOOKUP button" on step 6, not as a dropdown.

Correction to step 6: Check NULL checkbox on C2, and notice
that whatever is currently entered in C2 field has not been
cleared; then, click SAVE.

It seems that the content of the field has priority over
"NULL" checkbox, though I would expect it the other way
around: if NULL is checked, the field content should be
cleared when (or prior to) saving

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Moving back to bugs.

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Cannot reproduce your problem with your corrected steps, in
phpMyAdmin 2.8.1. I use this structure:
--
-- Table structure for table `t1`
--

CREATE TABLE `t1` (
`c1` int(11) NOT NULL,
PRIMARY KEY (`c1`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;

--
-- Dumping data for table `t1`
--

INSERT INTO `t1` VALUES (1);
INSERT INTO `t1` VALUES (2);
INSERT INTO `t1` VALUES (3);
INSERT INTO `t1` VALUES (4);
INSERT INTO `t1` VALUES (5);
INSERT INTO `t1` VALUES (6);
INSERT INTO `t1` VALUES (7);
INSERT INTO `t1` VALUES (8);
INSERT INTO `t1` VALUES (9);
INSERT INTO `t1` VALUES (11);
INSERT INTO `t1` VALUES (12);
INSERT INTO `t1` VALUES (13);
INSERT INTO `t1` VALUES (14);
INSERT INTO `t1` VALUES (15);

-- --------------------------------------------------------

--
-- Table structure for table `t2`
--

CREATE TABLE `t2` (
`c2` int(11) default '0',
UNIQUE KEY `c2` (`c2`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;

--
-- RELATIONS FOR TABLE `t2`:
-- `c2`
-- `t1` -> `c1`
--

--
-- Dumping data for table `t2`
--

INSERT INTO `t2` VALUES (9);
INSERT INTO `t2` VALUES (11);
INSERT INTO `t2` VALUES (15);