From the description, I get the impression that the designer's intent is that it can only freeze stuff that isn't normally hot. I say it doesn't affect lava. In D&D lava is a paraelemental combination of fire and earth, so it is not strictly earth or stone. Well, technically that's magma, but lava is just the name for magma that has reached the surface, it's the exact same thing. It's as much fire as not, and it's extremely hot, so no dice. Unless it's a 9th or epic level spell, in which case there might be fair reason to consider the possibility. Maybe a 7th or 8th level spell, but I dunno. Protection from Elements will only protect a single character from immersion in lava for 1-2 rounds; any spell of similar level is certainly not going to neutralize the heat of an entire mass of lava (even just a few feet deep) for more than a few seconds, and I doubt there'd be a 'freeze lava with ice' spell below 6th level at least (and only a very very brief freezing at 6th-level).