I was able to get this to stop complaining about flowbits by disabling the following
1:26470,1:50525,1:27544,1:58835,1:60270,1:60728,1:45952,1:49670,1:58812,1:55839,1:53858,1:46825,1:57452,1:61359,1:61360 # invalid signatures
1:28582,1:28583,1:28584,1:28585,1:28586,1:30990,1:30991,1:61666,1:61667,1:61670,1:61671,1:61672,1:61673,1:61674,1:61675 # flowbit set but not checked
After disabling all of the above I no longer get any rule errors on reload/restart.