BTW, I meant U.D. 3.3.1 in the Thread Topic Title..

But I believe I solved the problem on my phone for missing text message notifications. It bugged me that My handcent notifications were not working and I'd just have a unread text message just sitting in my inbox, not knowing i received one. I even contemplated on going back to 3.1 or even Froyo 2.5 but Im still on U.D. 3.3.1 so maybe I can help ya'll out on this..

First, I used a terminal command to set the memory management parameters back to stock Froyo.

This is the proper command:
echo "2048,3072,6144,7168,8192,8192" > /sys/module/lowmemorykiller/parameters/minfree

As seen as here, posted by GirLuvsDroid, Post #1007::
{ROM RELEASE}ProjectElite v5 Gingerbread AOSP

Second, I had auto killer.. and then I installed Advanced Task Cleaner from the Market.. I deleted auto killer because I didnt need it on my phone but thats optional to you but I figured it would still kill the Handcent app. What Advanced Task Cleaner allows you to do is ignore an app from being killed. So I long pressed on Handcent SMS, and chose to ignore this, as well as messaging and messaging widget [Yes, I know we can lock messaging into memory] So while advanced task cleaner is killing all other apps from running in the background, it avoids handcent SMS and messaging from being killed.

Third, I did set my minimum overclocking to 400 but 250 works too, seeing I just checked it right now and its on 250 and all my messages are working.
Also, Settings>Ultimate Droid>Performance>Check "Allow Purging Of Assets"..

Lastly, Unfortunately, I did have to start over with Handcent. If you restored Data to Handcent using TB, it probably won't work, but you can try. However, I uninstalled using TB, and reinstalled Handcent from the Market and started from scratch..

I rebooted into recovery because I WAS about to flash 2.5 cuz my notifications still were not working, but I thought, "Mind as well make a backup while Im here, just in case" so I did that, rebooted into Android cuz I was waiting on an important text, and Voila! Everything worked again. Notifications started to work again, there was no need to flash another rom, and I was back in business.