You can delete .DS_Store files with OnyX. Get version 2.4.1; the next one is still in beta. After installing and launching OnyX, select the Maintenance tab and then click Rebuild (that's where to go for the Snow Leopard version but I assume that the Lion version is the same). After doing this, the folder positions will revert to defaults but you can re-arrange them to your satisfaction. That re-arrangement should stick.
Jon
macOS 11.7.10, iMac Retina 5K 27-inch, late 2014, 3.5 GHz Intel Core i5, 1 TB fusion drive, 16 GB RAM, Epson SureColor P600, Photoshop CC, Lightroom CC, MS Office 365
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