Same here. Had the same trouble in 2005 as well - the whole of level two was missing and I got an assertion error.
An Assertion failed in
D:\Dev\Baldur\ObjCreature.cpp at line number 8786
Couldn't teleport in with a cheat code, either. Level 2 has Yeslick and Rill, so is quite important if you want to rescue the miners. I think Echon made a new copy of AR1802/04 available.
The funny thing is, is that this time through my Good party got to level 2 with no problem (Imoen, Coran, Jaheira, Faldorn, Garrick, Elf F/T) but my Evil party gets the assertion error - perhaps it's something in the save game file. The only difference is that the protagonist is CG in the Good party and NE in the Evil party. Plus the Evil party has Jaheira, Shar-Teel, Kagain, Viconia and Edwin. I can teleport to the 3rd level and complete the mine, but I can only flood the mine with the miners still in it. OK for an Evil party...
Bizzarre things like this happen with FotD. One time the Wyvern head description was replaced with that for a longbow. This time, the Cloudkill spell is replaced by the Ankheg plate armour description. There must be some unstable, randomised bug in the installation.
You also get assertion errors on the Gibberling map with the injured Samuel - this is one of the few maps Echon hasn't changed much as you still get the ring of fire resistance in the cliff face. I don't know if this is a corrupted install, though. As you go east towards the edge the game often CsTD with a creature assertion error
I love the "True AD&D 2nd edit rules" aspect of this mod. It makes you realise just how much Edwin really sucks, despite his bonus spells, and how a few invocations really make a difference. Next time, I'm taking Xzar.