I ran this section of the module a few nights ago and had similar issues with the cube. The problem with engulf is that it treats the attack as part of a movement-it moves 3 squares and anyone it moves through, it attacks versus their reflex.
I ruled it this way, and it was probably wrong, but made for a fun encounter. Because it is a cube that occupies a 2x2 area, it can hold 4 characters inside it at a time. If it engulfs, they are considered "grabbed" and can attempt to escape normally. If the cube decides to move, it must make the normal grab checks to do so vs. everyone's fortitude, and if it fails against anyone, that person is no longer grabbed. Because the party consisted of 5 players, I also ruled that they could attack it from within it's square, even if they were engulfed.
Now I have a lot of problems with this, listed below.
1. What happens if it's moving east and the character in it's northeast quadrant escapes the grab, but the person in the northwest quadrant does not? This would be greatly clarified by knowing if the cube can actually contain multiple characters or if I was just playing it incorrectly.
2. Do ranged and area attacks made while engulfed provoke attacks? I assume yes.
3. What exactly do powers that push/pull/slide do to the ooze if you are inside of it?
To be honest, we were only playing with the PHB, DMG and the module, so perhaps some of these questions are answered in the MM. This monster, if I played it correctly seems very mean spirited and frankly would have slain the players if they hadn't noticed it beforehand and it had been able to sneak up on them as the module suggests.
So I guess I'm looking for answers as well. The encounter ended after a lot of people took a lot of acid damage, but for my own satisfaction I'd like to know how this guy's supposed to be played.