Sorry about my anonymous response last time...
In the 2.40 beta 1 version, I'm unable to reproduce the symptoms you're talking aobut. No matter when I change my "Ignore first hops" option, things recover correctly when I change it to something else.
Can you bundle up a bit of data (if you use 2.40, you can insert some comments for me telling me when you changed modes, and what mode you changed to), and email it to [email]email@example.com?[/email] In 2.30.1, this feature wasn't always clean in the way it recovered, but in 2.40, it should be working more cleanly. In addition, it should be pinging the intermediate hops in *any* version that supports this - it's just that 2.30.1 would sometimes have a bit of packet loss reported (incorrectly) in the first sample set that came back with a full route.