I'm having the same experience; I've read a bunch of reports from people stating that their back pain vanishes, while I've found sometimes my (minimal) back pain can get worse on some days.

I don't have the option of swapping it around; my "standing desk" is a regular desk with cardboard boxes and telephone books stacked on top ( http://instagr.am/p/MUmlP/ ). At this point I can't get a new regular chair, let alone a high stool, unfortunately.

I'm giving it a week; after then I'll decide whether to switch back or not.