Have you looked in IN-A for the parent to see if there is an Average, Last or Standard Cost shown there? If so, you will need to fix that problem first. This can happen if you change an Item Type from, say Assembly to Kit. You would have to change the type back to A so you can edit the cost (IN-B) back to 0, then change the type back to K.
 
If that's not the problem, check your setup. I haven't delved into it for a long time, so I don't remember where it is or the options, but I know there is a place you can change how Kit items are Priced, and there may be something there about Costs as well. OTOH, if you've been using Kits all along and they usually come out right, that may not be the issue.
 
Lastly, I know there were some issues with the T7 version(s) of SO-E last year regards to Kit items. I don't remember the issue exactly, but if you're using the (T7) version I would suggest updating if possible, and if not, try the T6 version. I think the T7 one has been fixed, but we just don't like it and have stuck with the T6 one. One of the things we didn't like about it is the way it processes Kit items, and we do a lot of them - dozens every day.
 
Hope that helps...