Limit to relationship field entries?

[CPapadim]

I have a set of bidirectional relationships (this is a different set from issue #4687 that I opened).

This is between two custom content types, A and B. Content type A has just 3 posts, while B has thousands. So each of the 3 posts in A have thousands of relationships, while each of the posts in B will only have up to 3 relationships. When I enter a relationship from content type B to A (so in B's edit form), i can save it and this works fine. When I enter it from A to B though (so in A's edit form), it does not save it for two of the three posts. Furthermore, if I add the relationship to B, then re-save the A post, that relationship disappears.

I mentioned above this only happens in two of the three posts in content type A. Interestingly, the third post that doesn't seem to suffer from this has the fewest entries . Is there some sort of limit I'm hitting? Some sort of query length limit maybe or too much data submitted at once? It's odd that I can add it in one area but not in another, and that saving the post that is one-to-many relationships actually loses some of the data.