This is a known problem since the last major expansion/update of EVE. The cause for this (and related bugs) is not overly apparent, so it's going to take some trial and error to figure out a way around it. It SHOULDN'T happen at all.
It's the nature of a product like this that there will be expansions/updates that break things. Some are harder than others to fix. But, we usually finally find the cause and a way around it.