I've had no problems with my Eee 901 and heat. I run a ton of unnecessary Compiz effects too. Perhaps you need to play with the fan script? I know I had to do some hacks to get my fan to work on demand. I'm not sure what the difference is between the 900 and 901 anymore. I know mine has the Atom processor. I also upgraded the RAM to 2gb (so I could run Firefox and Netbeans off Ubuntu's built in ramdisk). I'm using the Array.org custom kernal if you are not already using it I would HIGHLY recommend giving it a shot as it may help with your problem. Also this is cool too if you don't already have it. Does a lot of the hacks I had to do myself the first time I installed Ubuntu.
Thanks I've been seeking for a special avatar I could use here for quite some time now... Couldn't make up my mind on one until I found this one. I guess only one image wasn't enough so this one is almost perfect even though it makes you dizzy, lol Hmm.. interesting colors for your profile, btw...
when I was like 13 and needed an email address, Lydia was my favorite first name, b was and is my favorite letter and the first initial of my favorite last name, and 6 was and still is my favorite number, I got lydiab6 and it has stuck