Are we talking about the same thing, gang?
For a start I don't think AnyDVD will remove FBI warnings (tell me if I'm wrong and I'll buy it). My understanding of that program is that it removes Region and CSS protection on the fly.
Removing warnings is a moving target. Some DVDs contain the warning in VIDEO_TS.VOB, in which case it's easy to fire up IFOEdit and invoke the 'delete playback' option in VIDEO_TS.IFO (see various guides on IFOEdit). Other DVDs make a jump to another titleset wherein lies the warning. If you delete that titleset - a la InstantCopy - the DVD will not work. It still has the jump instruction and, finding nothing at the end of jump, enters hyperspace. In these circumstances you need to modify the 'first play' option (as a minimum), usually to jump straight to the main movie. But, if you do this and then subsequently call up the chapter menu, you can still find yourself in the same predicament...
It is probable that because of the many possible scenarios, transcoder writers have in the main sidestepped the issue of removing titles automatically. There seems to me to be a gap in the market for an analysis tool which will parse the IFOs of a particular DVD and recommend changes. I might even write it myself!