I just finished setting up a configurable product composed of 3 attributes: Bag Color (4 choices), thread color (9 choices) and font (3 choices). 108 simple products were created and appear correctly in the database. Bag Color is unique to this product but thread color and fonts are used with several other products. All the other products sharing thread color and fonts work properly.
When I check this, newest product on the web site I have all 4 colors, and three fonts, but only 3 thread colors and that is consistent across all Bag Colors. I've cleared cache and reindexed several times. Still, all the records appear in the "Manage Products" page. It's as if the web page doesn't seem to be seeing the same records.
I went back into the configurable product "associated product" page and discovered the most strange part. When choosing the attributes sometimes all the thread colors appear in the dropdown, then other times only the last 3 are available. There is no "design" behind it, so I can't force it to happen. It's random.
I need to find a way to fix this without re-entering all these products. Worse, I am very concerned it could happen in the future.
I think the problem was caused by my changing the "Super product attributes configuration" order while entering the "assocuated products". What a mess!
I ended up deleting the items and starting over. At lest it is now up and running.