If some cross sells are NOT displaying, and you've changed product urls recently (e.g. for SEO purposes), then you might have broken cross sell links. This happens because Cross Sell uses product urls to reference products to be shown as cross sells.
To know if you're suffering from this issue and fix the problem, do the following:
1) pick a product that is not showing cross sells. In the example below we have an item called "Aromatric Massage Oil (2oz)", which is configured with 4 cross sells. However, only 3 items are showing (see images below). The item "Aromatic Massage Oil (8oz)" is NOT showing.
2) search for the missing item to see if it can be assigned as a Cross Sell. IF the "ADD" button is active for the item, then this indicates the cross sell's link is broken. To fix this, continue to Step 3 below.
3) Delete the broken cross sell by clicking on the X. This should make the cross sell disappear.
4) Click SAVE
5) Click on the "ADD" button for the item you just removed
6) Once the item shows up as "ADDED" once again. Click SAVE.
7) The items should now show up as ADDED, and should display properly as a cross sell again.
8) Repeat the process for all products missing/not showing cross sells.