either your;
velocity
zero
scope tracking
distances
atmosphere
or part, (or all) of the above has errors.
velocity - try another chronograph alongside yours on the same day next time, compare the 2, if they are both the same, then its most likely ok.
zero - obvious, but the distance your scope is zeroed at must be accurate, ie exactly 100yds not 107yds for example... AND your impacts @ 1000yds is much more important, the center of your group @ 1000yds must be in the center of your aiming mark before you really know how much you needed to dial. if your groups are large, then the center of this group can be difficult to determine accurately at long range. Once you think you have it centered, use a fresh target and verify it again @ 1000yds with AT LEAST 5 shots assuming a dead calm day.
scope tracking - most scopes have a significant amount of error in their "click value", even the expensive ones, but some are alot worse than others. To check how much error your scope has, shoot a 3 shot group at a dot low on a large target at your zero distance, 100yds is easiest for MOA scopes, 100m for mil scopes. Dial a healthy amount (say 25MOA or 8mils, more the better) of UP elevation on your scope, then shoot another group at the same aiming dot. This group will impact about *about* 25inches higher now assuming 100yds. Take a tape measure and MEASURE ON THE TARGET center of first group, to center of second group and then compare this measurement to what it *should* have been in terms of MOA or mils by converting the inches or cms to MOA or mils. Calculate your scope error from the difference. Again, make sure the distance your shooting at is exact, 100yds = 100yds true. Only 5% tracking error, = more than 1 MOA @ 1000yds.
distances- again, you need accurate distances, use a proper competition rifle range where the distances are measured out correctly, or a quality rangefinder if you have you own private setup (unless you want to physically measure out 1000yds the old fashioned way) The bigger the distance, the MORE CRITICAL this becomes. just 25 yds error at 1000yds from a 7mm = roughly 3 clicks. When you reverse calculate the BC, your calculating a trajectory thats 3/4 MOA flatter or rounder than it really is and you get a big difference in calculated BC.
Atmosphere - you need proper tools here; the humidity can largely be ignored, the temp is a little more important, but the pressure and altitude is very important. Make sure you got correct values here.
The BC will end up much closer to .531 if you check everything above and find your errors.