I haven't ever had to use the "back apply" average/handicap thing, and I don't have my Windows laptop (with manual) handy. But to back-apply, it may be necessary to go back to week 1 and then return to the current week to get the back-apply to be appropriately used in the early weeks. Again, I don't have experience here nor am I in a position to experiment with a test league, so I can't say for sure that this is how it needs to be applied, but this is what comes to mind.
If you need a different average/handicap applied in earlier weeks, you can always go back and override the individual bowler's average and/or handicap, though you'll have to do it for every game in the series for every week necessary. It's a bit tedious, but it would get the proper handicap score to show. This is something I've had to do in the past.
Always check, download, and install the most recent update of your software to ensure that issues may have been corrected.