Hey, Jerry.
I set up a similar test with version 2.61 and see the same results you do. I tested on the same server with version 1.27 and didn't have a problem.
I changed the following image quality setting and the transparency was fine at any size thumbnail.
FILE: /lib/image_functions.php (approx line 63 & 64)
// resample image
$quality = 4; // v2.60 Speed up resizing (was 5 previously)
Here I changed: $quality = 4; To: $quality = 5;
I can't say what impact the quality difference would have on a site when uploading or batch resizing a large quantity of images, but maybe upgrading the GD library on my server would accomplish this task with the lower quality setting. I didn't have time to look into that further, but maybe this will get you where you need to be today.
Hope that helps.
~ Deborah