After ignoring this issue for so long, it's finally time to ask...
When ballooning, the balloons sometimes do not match the BOM. They show the lowel level component and not the sub-assembly they're in and being shown in the BOM.
The BOM Type is set to Top-level only. The sub-assembly's configuration properties are set to Show for "Child component display when used as a subassembly". (For all configs.)
Also, after ballooning, the 'indicator column' doesn't show ballooned status of components. Balloon settings are Balloon text: File Name. Part Number (BOM) also shows the component and not the sub-assembly.
How can I fix both of these things? (Balloon display and BOM balloon status)