Without having the discs to look at I'm just taking a pure guess here but it's probably something to do with BD-J / Java.
VLC is very good but it's not perfect and without a version of Java it's happy with installed on your system you may find some discs don't 100% function as you might want them to.
I've not messed with my setup for a while because it "just works" currently but I'm pretty sure more recent versions of Java don't work properly with VLC (or maybe it's vice versa?!) and I ended up installing an earlier version which fixed the discs I was having problems with due to BD-J.
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