I've got some pretty complex graphs on a few of my DB's (have to print them on 11 x 17 paper to get it all on one page.) and haven't seen any such problems.
Are the cases where your relationships are failing direct table occurrence to table occurrence relationships or are they cases where filemaker has to trace a relationship across more than one "in between" table occurrence?
TO to TO relationship:
Table1::Key = Table2::key
Relationships spanning multiple TO's:
Table1::Key = Table2::key = Table3::key
Where data in table 1 fails to correctly link to data shown in table 3.
I can see problems in both -- I do have some relationships that go through 5 or 6 links. (These get displayed in portals, of course.)
I am emulating Object Oriented Design according some of the advice on the Web, so most records are an extension of a base Entity record, the serial number of which serves to tie together extensions of Objects.
This turns out to have been a corrupted database. Invoking "Recover" from the "File" menu yielded a correct file, even though the recovery log claims that no changes were made (and the "Check Consistency" claims there were no problems).
Recover should only be used to retrieve data. Once a file has been recovered, it should never be used again. You should instead go to a backup copy of your file (to a point before the file was damaged). We have been imploring FileMaker to make this clear in their documentation and stance. There are threads about it where they admit (in posts here) that one should never use a recovered file but it isn't obvious to the regular user.
Just as the logs didn't indicate damage that it fixed, it can not indicate damage that it can't fix. It is simply not to be trusted. If you continue working in a recovered file, you can find it out too late and you will have to trash the file and go backwards anyway. Better to do it now than after you've continued working in it for another six months.