Hi magnus,
I discover that the textfield didn't have an id tag
I added a extra parameter to the text area creation in the file admin/categories.php:
,'id='.$languages[$i]['id'].''
Original
<td class="main"><?php echo tep_draw_textarea_field('products_description[' . $languages[$i]['id'] . ']', 'soft', '70', '15', (empty($pInfo->products_id) ? '' : tep_get_products_description($pInfo->products_id, $languages[$i]['id']))); ?></td>
so it becomes:
<td class="main"><?php echo tep_draw_textarea_field('products_description[' . $languages[$i]['id'] . ']', 'soft', '70', '15', (empty($pInfo->products_id) ? '' : tep_get_products_description($pInfo->products_id, $languages[$i]['id'])),'id='.$languages[$i]['id'].''); ?></td>
And then the ckeditor works again.
Since there was no id in I guess adding it doesn't harm anything.
There might be a more elegant way of solving this since this just fixes the text area when adding or editing a new product.