I've been encountering this very recent bug for llSetLinkAlpha (and even for changing alpha with scripts in link sets). If you use LINK_SET, llSetLinkAlpha will work fine, and invis or uninvis everything just fine, but if you're trying to alpha in specific prims in a set, it starts to have issues, even with small sets of only 30-50 prims.
When you try to invis prims, they'll 'stay' on the screen, but as soon as you right click the set to highlight it, the visibility of the link set corrects itself to what the script tried to set it to, which makes me wonder if there is a client bug dealing with the alpha.
Has anyone else been encountering this, and is there a way to sneak around it in the meantime? It's been plaguing me for months, and I've tried everything to get around it, including using llSetLinkPrimitiveParams, etc to no avail; it really seems to be a client side issue with all 1.23.X clients.