Of course album photos show up in categories. What else would the "copy to category"-function be good for? That's what we are talking about in this thread, are we not? This was never about assigning whole albums to a category, but about assigning single images to a second category.
Obviously, I did not fully analyze the code. But the index pages of categories are called by showgallery.php, and that's where the changes are made. After the changes, the single photos copied to a category from a User Album are not shown in the index of that category any more. If you say that there can be no connection, I have to say that there has to be, since this is the only change I made to showgallery.php and I'm able to switch this behaviour on and of by applying and removing the code changes.
O.K., let's see, once again:
I have a single Photo. This single photo I upload to my User Album (showgallery.php?cat=564) and at the same moment I copy it to a category (showgallery.php?cat=502).
If I leave showgallery.php unpatched, I see the single photo in my User Album and in the index of the category I copied it to. But: If I use the "Last x days" function, I see the photo twice.
Now I apply the patch to showgallery. The "Last x days" function now works perfectly well, and I can still see the photo in my User Album. But it has vanished from the category index now. If I call the category index (showgallery.php?cat=502), the photo does not show up anymore. Once again: This is not about assigning an album to a category.