If the cap jewels are seated correctly and you have not transposed them then the balance is not aligned correctly. Rule of thumb DON'T FALSE ANYTHING. By any chance when you removed the balance cock for cleaning was there a shim between the cock bridge and plate. Sometimes if a new balance staff is changed and it is bit tight a cheats way is to put a thin shim under the cock.
I'm not familiar with the tool you are using, but it looks like it is giving good results.
Screwdrivers are more forgiving than knives with shapening, to sharpen my screwdreivers I purchased a 240 grit and 400 grit diamond sharpening plate off ebay for just $3 or $4 each and have one an A&F spring loaded screwdriver holder for sharpening and find that gives me pretty good results.
The most important thing is using your Loupe to check you have inserted the screwdriver correctly before sharpening.
Also if you are removing a chip on the blade you will normally have to hold the blade at 90 degrees to the diamond plate and take a small amount off the end so they screwdriver blade once sharpened to ensure it doesn't bottom out in the screw.
Did you remove the cap stones on the balance and fully clean out the old oil?
If not the old oil could be gumming up the new oil.
Have you checked the pivots of the balance for wear?
Checked the jewels for any cracks?
Does the anchor snap cleanly from side to side if you nudge it with an oiler with the balance removed?