Over the weekend the builds tool was updated to reflect patch 2.4.1, as you might have noticed. However, it seems like not everything went as smoothly as we hoped. There were a few bugs and most have been fixed, but please post here if you think you encountered other issues.
One bug was that some set items disappeared. While that has been fixed a few days ago already, the set items can't be put back into old builds - sorry about that; the information just went missing in the process and therefore the build tool doesn't know which set items are supposed to go into the empty slots. If that bug happened to you, please put the set items back in that were deleted by the builds tool transition.
Another issue seems to be that some items are missing and/or can't be selected. For example:
Henri's Perquisition can't be selected for off-hand
Dagger of Darts seems to be missing entirely
Royal Ring of Grandeur can't be selected in cube
Crudest Boots not listed in cube powers
Three Hundredth Spear not listed in cube powers
If you find other items post here - those are the ones I've discovered myself or have been made aware of. Also check this thread.
Apologies for the inconvenience, and thanks for everyone helping us to figure out the small little bugs here and there. In the meantime, have fun with the start of Season 6!