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I know it saved because a) after every encounter/mission/activity/etc. you complete, the game audosaves and b) it says, "12 random encounters met" but there are only 14 in the game (fortunately the guide says only 10 are necessary).
As for everything else, I checked my list.
Storyline Missions - 60% in chunks of 0.66% - All 94 missions DONE.
Assassination Missions - 2% all at once - All 9 missions DONE. Brucie's Races - 2% all at once - All 20 Races DONE. Brucie's Exports - 2% all at once - All 10 exports DONE. Stevie's Car Thefts - 2% all at once - All 30 thefts DONE. Little Jacob's Deliveries - 2% all at once - All 10 deliveries DONE. Current Crimes/Vigilante - 2.5% all at once - All 20 criminals DONE. Most Wanted - 2.5% all at once - All 30 PEDs DONE. Random Encounters - 5% in chunks of 0.5% - All 10 (plus 2 extra) encounters DONE. Activities - 5% in chunks of 1.67% - Played ALL games with everyone, all activities with everyone, won against everyone in every activitiy, etc. DONE Special Abilities - 5% in chunks of 1.67% - All three special abilities (Helicopter, Guns, and Bomb) DONE. Competitions - 5% in chunks of 1.25% - Won at pool, bowling, and darts. It's even recorded I won them (more than once). Also, high score at QUB3D (my score is 11,275) DONE. Flying Rats - 2.5% all at once - All 200 pigeons DONE. Unique Jumps - 2.5% all at once - All 50 jumps DONE.
I replayed all the man-dates with everyone more than once. Heli-rides, shows, strip clubs, pool, bowling, darts, etc. EVERYTHING but coming up flat. I just don't know what I'm missing. I really, really don't.