The new percentage price modifications are not working for me. It sets all prices to 0.0010

Same happens to me.
See my post above. Make sure you are modifying using 100 percent as basis (e.g. 105 or 95, not 5%). If that doesn't help you may need to recreate the plans, that's the only thing that worked for me after it got stuck at 0.001 and even a 500% adjustment couldn't move it.
Even with percentage (eg 105 %) it doesn't work. I thought that it will with decimals (1.05), but it put everything to 0.0010. Had to recreate all plans from the begging.