I am running Views Custom Field 6.x-1.x-dev, and had the same results with 6.x-1.0. I am using Views 6.x-2.16.
I use Views Custom Fields to display a fruit, either red, yellow, or green, depending on the values of product stock, by this code:

<?php // hwd add color fruit for class full status
	 if ($data->uc_product_stock_active == 1) {
		 if ($data->uc_product_stock_stock == 0) { // no seats left
		   print "<img src='/sites/all/themes/cclass/images/symbol_red.jpg' alt='No seats left in class'><br />";
		 } else if ($data->uc_product_stock_stock <= $data->uc_product_stock_threshold) {
			 print "<img src='/sites/all/themes/cclass/images/symbol_yellow.jpg' alt='Only a few seats left'><br />";
		 } else {
			 print "<img src='/sites/all/themes/cclass/images/symbol_green.jpg' alt='Seats are available in class'><br />";
		 }
	 }
?>

The products are classes. When a class available seats is less than the threshold, the fruit changes to yellow. When the class available seats is 0, the fruit changes to red. This custom field appears in both a class listing and in a calendar.

This has worked fine for a year. However, recently, some classes have begun repeating in the views listing, with the first instance always green, and the second instance the correct color. The Custom Field handler in the Views UI under Fields has disappeared even though the field still shows in the view.

In the calendar, the class appears only once, and the color is always green regardless of the correct color.

I tried to add a custom field handler back into the class listing, and now the fruit appears TWICE! And when I refresh the Views UI, the field handler again disappears.

I tried to turn off the Views Custom Field module, and the custom field still appears in the view, while the calendar correctly reports in the Views UI that the handler is missing.

I read http://drupal.org/node/1362372 which indicates a problem between Views and Views Custom Fields. Could the Views 2.16 version be interacting with Views Custom Fields? I did upgrade to Views 2.16 but I can't be sure that this was when the change started.