I have made a post on the community recently this year about an issue which causes a variance between inventory module and general ledger in Dynamics GP when an enter/match partial cost modification is applied from the Purchasing Module. The case is a result of different GP modules' behaviors and it is thoroughly illustrated in the post below;
GP2010 SP4 “Issue Resolved” - Enter/Match Partial Cost Modification
Fortunately, the issue was resolved with the release of the latest GP2010 Service Pack 4. In this essence, I am sharing this post so that hopefully I could shed a light on further GP version, GP 2013. As the case is still open.