Running on Vista x64, so I've already limited memory to 3072, running in compatibility mode for 98/me.
Whenever I start the game and the intro movies are playing the game minimises and if I alt-tab/click back in - crashes. I have to wait until the movies are over before i can get back into the game. Also, sometimes ingame the sound will cut out and I have to restart the game to get it back. Has anyone else come across these problems?

I would suggest updating your video drivers if you have not already. I believe you already said you installed as an admin and have checked the "Run as an administrator" in the game shortcut.
What CPU are you running?

Hmm this is odd, just ran the game without bothering to limit memory and the cutscenes ran fine, game started with no problem. I could swear that the slowdown was less than usual but that may be due to a scarcely populated level.
I'm running an E8400, tried with affinity set to one core and both, makes little difference, also running as an admin.

Some things you could try if you haven't already :
- limit the memory to 2048
- disconnect from the internet and disable all background tasks
- if you've got a codec pack installed add the Beyond Divinity executable to the exclusion list.

Yes, the game seems to run better when there is no lava or water around without limiting the memory. At the very start of the game, there is a lot of lava around, so people run into the slowdown problem very quickly unless they have saves from an older computer.

Great to hear you got it worked out. With the memory limitation I would think you would need to close all programs when playing since you have a small amount of memory available.