Squadgy - sorry I haven't had a chance to catchup with the forum for a few days. Nice to see you have positive results.
I don't know if you want to try a few more things with the fan-fold, but here are a few more ideas I have had (these are of course all theoretical as I don't have a printer to verify!)
I have looked at some Zebra service manuals, but not LP2824 (couldn't find one). In all the ones I have seen, the mark/web sensor is located in the exact centre of the print mechanism after the print head. This would probably prevent it from identifying a mark near the edge of the media (in fact some of the user guides state something like this in relation to the mark (not web) sensor). Also, thinking logically, in the Zebra any index mark must be on the leading part of the media to prevent mis-identifying anything printed as an index.
I am assuming that the large black mark on the lower trailing edge of the printed strip is the pre-printed index (the IER512 sensor is located before the print head).
I think you may be able to identify this mark by printing with the strip loaded in the opposite direction, however you will need to use a few other tricks!
Is it possible to set up the guides so the strip is offset, and the mark passes under the centre of the print mechanism?
You will need to select 'web sensing' in the printer set up to use the upper sensor. You will also have to increase the (theoretical)media width to compensate for the offset, and use the page margins to set the print position appropriately.
If it does identify the mark you will probably also need to use the backfeed setting to move the strip back a fraction before printing.