The bit which says whether or not to merge data during an import or export was incorrectly migrated for some users who upgraded from version 2 to version 3.  This causes:

1.  During exports, all items are being replaced in every time they export, typically causing their Safe Limit to be exceeded.  After a second manual export, the status bar will indicate something like +37476, Δ183, ↖0, ↕0, -37476 (many changes) instead of the expected +0, Δ0, ↖0, ↕0, -0 (zero changes).

2.  During imports, duplicates are created.

This issue is now fixed in BookMacster, Synkmark and Smarky version 3.0.3.  To get it, launch the version you have and click in the main menu under the app name: Check for Update.