Workaround:
If you can't resolve the issue, you can try to use form leaders to feed your printer with a proper 8.5x11 sheet while printing a partial 1- or 2-checks page in normal portrait orientation.
See https://intuitmarket.intuit.com/fsg/businesschecks/formleaders.aspx for an example of form leaders. Check your local office supply store, search on the Internet or order from Intuit.
My 2cents' worth: I use Voucher checks (1 business size check + 2 stubs on an 8.5x11 sheet). My printers do not have a manual feed tray or 2nd paper tray that can easily be reconfigured to feed partial pages (1 or 2 checks left from a 3-checks-per-page sheet), so for my occasional check printing needs voucher checks are easiest to use. When considering your own check stock to use, consider how easy or difficult it is to feed special forms or odd-size partial pages into your printer when making a purchase decision for a new supply of checks.