You probably have a number of variables that are adding up. The first is your environmental data,... sounds like you're working on getting that figured out - I wouldn't toss my iphone app 'til I'd tested it thoroughly with a Kestral or other weather station - not sure how your ballistic software is configured, but I'm assuming it will allow you to input Density Altitude (DA). Another key variable is your velocity. As great as modern chronographs are (I own two), they're not as accurate as we might like when attempting long-range, trans-sonic shots,... that's why you really do need to validate your drop at distance. The Ballistic Coefficient (BC) of your bullet "might" need to be tweaked, but if you're using Litz's data you're probably as close as you need to be. If you're using the bullet manufacturer's BC data, then I'd definitely look at adjusting that as well,... but play with velocity first. Also, just double check EVERYTHING you've input for your rifle,... sight height, twist rate, etc. The software is the software,... garbage in, garbage out,... Having owned half-a-dozen different ballistic calculators and played with a dozen more, I'm 99.9% sure that it's the inputs you're making,... Best of luck!
Ry