What versions of ArcSDE and ArcGIS are you using?
We had trouble to manage the srid for our FCs when we were in SDE 9.3.1. After upgrading to ArcSDE 10 and ArcGIS 10, it seems the only auth_srid matters. I think it is the spatial reference factorycode.
If you use SQL geometry, it doesn't matter what the srid is, as long as your FCs use same auth_srid, the SQL spatial functions/motheds will not fail. Whether it will give you the result you expect may still depend on other parameters (I am not 100 percent sure), such as falsex, falsey, etc.
Thanks!