I've just setup, and on rez some cuffs are out of position. Even after I've repositioned them, a new rez are still out of position.

After repositioning the cuffs, you find that subsequent newly-rezzed do not remember the edits. The most common cause is that SL has somehow made some scripts go comatose in a way that they half-work. The fix is:

1. Say "/1.quickreset". 
2. Then re-adjust the position.
3. Detach the cuffs, and rez another set to see whether it stays. If it still doesn't stay...

That should fix things. If it still doesn't work, then the SL borkage is probably worse-than-expected. In that case,

1. Go to the Secret Warehouse and get a fresh Update set at the Update Swtich. Then setup normally. 

That should work.

Thanks to Tyee Maximus for reporting this.