Ah, they joys of TinyMCE. The lovely editor will sometimes insert a line of blank text into the 'PHP Code' window of your custom content kit (CCK) type, this causes an eval() statement to break - you may see an error in your logs along the lines of :-

[Sat Feb 14 11:15:16 2009] [error] [client 64.39.0.38] 
 PHP Parse error:  syntax error, unexpected '<' in 
 /var/www/vhosts/yourdomain.com/httpdocs/modules/cck/content.module(1638) : 
 eval()'d code on line 1

If you have display_errors turned off in PHP, eval() can return a 500 Internal Server error header. This will mean Google and any monitoring software will receive a 500 error despite the site seeming to display normally.

So, to solve, head to

site building -> modules -> list

Turn off TinyMCE and save.

Then head to

Content Management -> Content Types -> Edit *your content type* -> manage fields.

Check the PHP Code area of each field for some text that TinyMCE may have dropped in there, delete it. Reenable TinyMCE problem gone!

Now resubmit to Google and breathe a sigh of relief :)