The whole issue generally is that the Amiga boots so fast with some accelerators, that the drive isn't at it's "ready" state when the Amiga polls for bootable devices. (Actually, this isn't a new issue, it's been around for ages, even for A1200's without accelerators, due to drives that take longer to spin up, and be able to do it's self diagnostics...)
Adding a small wait to let the drive spin up is all it takes. The same issue is, as i said, present with my CF as well, even as it has no moving parts. Weird, but i guess the logic needs a moment. Hot-boot generally avoids the issue since the drive is already spinning, the logic is fired up, and it's not doing any diagnostics.