If you look at the Gift Detail tab in the Fund module, those gifts should be summarized by GL Year on the Summary tab. If you are looking at a Non-Gift (an amount followed by NG), this will not appear on the gift summary. However if you have actual gifts that do not show on the summary tab, this is probably the result of an old bug that has been fixed in a fairly recent version.
To correct this discrepancy, you will need to run the following tool:
Tools > System Utilities > Admin Utilities > Rebuild Summary Tables by Year.
Here, you will choose your fiscal year range and module. If you run it for all years and all modules, it may take a while longer, but it would behoove you to include it all at some point.
If this does not correct the problem, contact FIMS support.