Conversions tend to work very well if no complicated features are used. As soon as tables get thrown in, you have to have an ebook that was built very carefully to begin with -- and it needs to be designed to work on each device/format combo or you are asking for trouble. Or so I've heard...
In other words, the problem could just as easily have been the other way, if things had been different.
There is a reason professional ebook makers (the ones who actually do what they are paid to) charge a lot. Hang out in the Vent and Rant thread, or the Workshop forum, and you will be privy to many highly entertaining rants by @Hitch, who does this for a living.
The ToC is a rather simple feature, and should be correctly converted almost all the time (but sometimes people do really weird things to them
).
MOBI to anything else will probably give the best results -- because you cannot do a lot of complicated things with them, so it will only have stuff which converts cleanly.