We have an issue logged with Sage support, where CRM has always got its context confused and it's never been fixed - happens when navigating Custom Entity 1 > Company > Custom Entity 2. 

The scenario is two custom entities built using the entity wizard and are a 1-to-Many relationship with Company. 

We can go from Company > Custom Tab 1 > click into a record > then click on the company name on the record to go back to the company > Click on the tab for entity 2 and sudden we're looking at a completely different company and the entity records shown are for this other entity (but we get no error messages like you, we just end up looking at the wrong company)

So whilst not completely like your set up, there is something going on here that CRM just loses where it is. 

We have an issue logged with Sage support, where CRM has always got its context confused and it's never been fixed - happens when navigating Custom Entity 1 > Company > Custom Entity 2. 

The scenario is two custom entities built using the entity wizard and are a 1-to-Many relationship with Company. 

We can go from Company > Custom Tab 1 > click into a record > then click on the company name on the record to go back to the company > Click on the tab for entity 2 and sudden we're looking at a completely different company and the entity records shown are for this other entity (but we get no error messages like you, we just end up looking at the wrong company)

So whilst not completely like your set up, there is something going on here that CRM just loses where it is. 

Maintaining context when moving between custom entities and standard entities has always been problematic for as long as I've done custom CRM work.