Please Also Refer to Bug Report 9049 :
I believe I am having the same problem. I think I have worked out why tho.

I have two files.
One has a function in it.
Both files require a connection to mysql database.
Both connections use the $conn as their pointer.
If you mysql_close($conn) within the function in the second file
then it closes the $conn in the script calling the function.
So you have to remove the mysql_close from your function
and even the $conn=mysql_connect from it and just pass the
$conn as a variable to the function :
eg
function foo($conn){
$result=mysql_db_query("test","select ...",$conn);
}
called from say test.html
$conn=mysql_connect("localhost","rootme","noway");
foo($conn);

was like this :

function foo()
{
$conn=mysql_connect("localhost","rootme","noway");
## query work etc..
mysql_close($conn);
return;
}

main script :
$conn=mysql_connect("localhost","rootme","noway");
#anything in here
#call function
$wotever=foo();
$result=mysql_db_query("database","query",$conn);

the last line brings up the error about the mysql link resource being wrong as the $conn was closed in the function but somehow closed it globally too. Which is a bit of a pain as this was ok before upgrading to Pl4

I didnt see anything in the change file about this :L So I can only assume
this is a bug.

If you need more info from me please let me know.. Thanks for all the good work guys :)