Try starting a new game see what happends... Also you can load your save game, fast travel somewhere, spin the camera around, then press ESC an load the save game again, 2nd load up usually is better performance. No not everytime but if you notice performance issues then yah. Then also did you run the 1.7 game patch, you should even if you have GOTY edition. Then the tweekguide can clear up many issues as well. http://www.tweakguides.com/Fallout3_1.html
The tweekguide does downplay a few settings which would help though. This is because it's a very old guide before there were tons of mods like today. Okay so the first setting it downplays is the background loader, I've seen no direct links to issues it causes. The 2nd one is bSelectivePurgeOnFastTravel if you turn this on it will cut out about 99% of the manual PCB (purge cell buffer) you would need to do to keep having high frame rates. As noted by you launched the game played for 30 minutes an now it's got grapical lag for some reason, yah PCB, but don't use a mod to do it. You can also manually PCB open the console an type it an hit enter. 3rd setting is bPreemtivlyUnloadUnused which is somewhat like the other setting but doesn't require fast travel to trigger it.
Sometimes games just don't start up well, this can happen later on too. This problem you have can also just randomly happen from something going on in the distant LOD where you can't even see. It's not permanent, an doesn't happen often. In the last two years it's only happened to me once.
Disable your autosave, then never quicksave either, press Esc each time an create a new save, an don't delete them until you are ready to delete them all. Also you might try runing two charicters at the same time. Then when one dies bounce over to the other, such is a nice way to doulble load into a save game. The continue button on the main loading screen is somewhat prone to coruption just like autosave an quicksave can be, so we don't use it. But if you have two save games you can load into one or the other an not miss out on any chance encounters from double loading a single game once. Also you get more charicter playthru one of them is nice the other mean, or maybe one is a slave the other a combat. Head on over to the official fallout 3 game website then look in the vault there is a diary about charicter playthrough, really nice general ideas..