This was a issue in both Greedy Mouse and Karma Miwa, why im dosent like this command at all. Its simply dosent work with alpha at all, due im got this issue again:
(http://dl.dropboxusercontent.com/u/3236515/glbasic/alphamultiply.png)
This issue have been there in years and still not have seen a fix. This cause this command quite useless in most cases.
Howover if CLEARSCREEN could been cleaned with a ALPHA value (CLEARSCREEN RGB, ALPHA), then im thinks this issue could been fixed, also eventuelly on the SMOOTHSHADING its self. IM do more believe the blend mode is wrong, since im have NOT seen this bug in BlitzMax.
Strange, I think I have stumbled on this before too, but it was more a file problem instead.
Can you post one of the images of those sprites so I can take a look?
The image did use any sort on alpha itself with transpanrancy background. It's was a issue in both other games as well.
My guess is the alpha here got inverted if there is alpha on them.
If there is a mem2anim() command, then this could have been workaround too by invert alpha values in its array.