I have recently just posted this issue in the bugtracker but I've also decided to post here to see if anyone else is having the same issue or if anyone else knows different ways to fix it:

Incomplete achievements are shown as complete with things like 100/100 but still grayed out. This is important because for as long as it shows this incorrect message it fails to record/count its true progress. For example, if you're going for the 100 Honorable Kills achievement and you have 43 kills, it will be shown as 100/100 but also shown as incomplete; any kills that you get will NOT be recorded. This issue inconsistently resolves itself on re-log, sometimes requiring anywhere from 2 to 20+ re-logs to fix. (Note that this fix does not add on any progress made during the time the counter was bugged, it just goes back to counting from where it was before.)

This issue appears with any achievement with quantified progress. One of my suspicions is that this can be as a result of the AT + molten merger for Warsong because my character was made on old AT, or because of the bugged statistics tab which shows everything as 1473623621631.