I think I know what your problem is: the too-may-items bug. Info from the
Nearly Ultimate Fallout 2 Guide:
The too many items bug
I don't know exactly how it works technically, but what happens is that late in the game, if you have too many (different) items in one location, this will eventually corrupt maps. The number of items in question includes what you and your NPCs are carrying, the items on critters and in containers on the map (including shops), plus the stuff in your car no matter if it's present or not. The bug triggers upon leaving an area, and means that next time you try to enter that map, your computer will lock up completely. Many people have reported this behaviour; you'll notice how the "orbiting rocket" mouse pointer shows up on the screen, but doesn't animate. The hard drive might buzz for a while then fall silent. Depending on your system you may have to turn your computer off entirely. If you reload the game the same thing will happen again eventually, or right away if the save includes the broken state of the map you're trying to enter (but since a map goes bad only when you leave it, the current map of each save will never be corrupted, thankfully). Maps will become corrupted more frequently as you continue to play and amass items, making the game nearly (or literally) unplayable towards the end.
The simplest way to prevent this from happening is to avoid carrying around quest items which you have no further use of. If you want to keep them, don't store them in your trunk but in some accessible container on a map where there are no shops, or where there are not too many items anyway. If you want to be doubly safe, avoid selling too many different items in one place. If you're not in the habit of hoarding items, this will probably not be an issue.
If a map in a saved game has been corrupted, there is no way (known to me, at least) to restore it, but you can work around the problem. What you must do is find the corresponding file from an earlier save and replace the bad file with it. For instance, San Francisco Chinatown, which is the map where this might well happen to you the first time (two big shops), is "sfchina.sav" - use the Ctrl-R trick to find the right map if you're in doubt. Critters and items on the map will revert to what they were in the previous save, and local variables may change (possibly interfering with dialogue or allowing you to repeat certain actions), but global variables such as quest status as well as the contents of your car are stored elsewhere and so are not affected. NPCs (including the trunk) left standing on the broken map will only be present if they were in the save you got the replacement file from. (You may also on the "fixed" map encounter duplicates of party members left behind elsewhere, and you can kill these and take any stuff that the real NPC was carrying, but this would be cheating.)
At this time it's not perfectly clear which circumstances lead up to the freezing bug. It's been theorized that having too many Pipboy files in your status screen could be the cause of the bug, since it can lead to the "black button" bug and would be consistent with the fact that it strikes after visiting the Military Base with its holodisks. It's also possible that there are multiple causes for the black button bug (which has even been observed in the original Fallout as a result of excessive item hoarding), but that only in the "too many items" case does it go on to the freezing bug; to my knowledge there are no reports to the contrary.
Daniel Valle may have found a way to circumvent the problem based on the theory that the corruption bug only follows the black button bug: "I noticed that the skilldex button going black happened only after I opened the Pipboy and checked out the status screen to see my missions and logs. Opening the Pipboy's primary screen or alarm clock did not cause this. My solution has been to not look at the status screen. If I really had to do so, I would quicksave and check it out, then I'd have to shut down the game and start it up again, because once the skilldex button's gone black it will stay black, even if you load save games from Arroyo, which could possibly corrupt maps even early on in the game. So far it has worked well on two games I have already beat and one I am still playing. Truly, I don't know what triggers the problem or its true cause, but if this keeps the game from locking up and corrupting maps then it will have to do."
