Was about to write a post asking for help now it appears i have a solution that might work for others.
Was having problems migrating settings from old compy with 2015 sp4 to new compy with 2016 sp3. Didn't bother to upgrade old compy first, which might have saved some headache. Seemed to be an issue with .sldreg file continually writing a new sw 2015 folder into the registry for the changes and not touching the 2016 reg entries (even though new compy hasn't had any previous SW versions installed)
This blog post got me part way there, with one notable difference: CATI Tech Notes: How to Copy Your SOLIDWORKS Settings Correctly When Upgrading to a New Major Release
Its important to NOT open SW after the registry folder rename, unlike the order of operations stated. rename the SW folder, then dbl-click the .sldreg file, deselect system options, THEN run SW 2016. It will pop up a few warnings about changes it can't apply regard command mgr buttons and menu customization, ask you to accept the EULA again, then seems to work just fine with my old shortcuts, toolbars, etc.
Hope this helps.
Not sure if it is just my improved graphics card, but i'm liking the looks of 2016 so far.