Having a similar problems. Parachutes break off when just re-entering with just the command pod making it impossible to retrieve science. If I leave just a fuel tank and rocket on, it makes it through the atmosphere and I can deploy the chute. In 1.02 this was working fine and I could capture the command pod and get the science credit for it. Tried the same in 1.04 and the command pod just wouldn't slow down enough to land safely, it would crash going 40-50m/s every time where the same exact configuration(while reducing the re-entry heat so I can actually survive re-entry without extra heat shields since they don't come till MUCH later), same ship save, same situation would slow to 6m/s under 100m on 1.02. I don't know, something seems off in 1.04. Might be the save conversion. Noticed in 1.02 the parachute would deploy at 500m but in 1.04 they deploy at 1000m. Thinking if you have a ship save from before, it will hold those old version default values for parts and not accept the new version values but I never got to check. Drag, or atmospheric density or something also seems to have changed drastically in 1.02 to 1.04. In 1.04 I can hit over 9000m with just a single RT-5 solid booster but in 1.02 I can barely even hit 4500m. While that's great for getting out of the atmosphere, its extremely deadly for re-entering. You just don't slow to terminal velocity falling through the air any more, or at least not quick enough. I think I'm going to stay at 1.02 for a while since 1.04 sacrifices fun for "realism". While it does seem like it would be more rewarding, if I spent days upon days trying to get something that can survive re-entry, its just not why I originally bought KSP.