I've got a few complex script that run in a few windows at once and do some tricky stuff to records. The problem is that I get a lot of "You can't edit this record because it is open in another window" errors.

Is there any simple way to stop this from happening, to tell a script to stop editing the record without closing the window. Would it be easier to post the entire script to find out where the problems lie?

The "Commit Record/Request" script step is your friend. Invoke it when you have finished editing a record.

In this case Commit Record should be used at each change in focus to another file or window. Committing the open record allow you to then edit the same record in another window.