Hi Sean,
Are you using v201502, v201506, or v201509 of the AdWords API? Also, if you happen to have report output that demonstrates this issue, please send it over only to me by clicking Reply private to author on this post. I've tried several report requests on my side and so far I haven't been able to find the discrepancies you mentioned, so having the output you're seeing would be helpful.
Thanks,
Josh, AdWords API Team