I'm having a similar problem with FM12, please let me know if you have come up with a solution.
Something has changed regarding rendering work (graphics AND data's) with FM12v3.
This issue I posted showed up with 12v3 first and might be related to this one anyhow:
I had same problem and solved it with Portal Filters. Remove filter from join relation and put this condition into portal filter calculation:
And upgrade to 12v4
The portal filter must be refreshed with script trigger on ContractFilter Checkbox - On object modify -> Refresh. If you can't flush cache, look into this file: https://www.sugarsync.com/pf/D755741_69660782_474742
this problem seems to be solved with v13, so good news for those who did the upgrade.