My A4000T has about 10 seconds delay on boot when it starts to read hard drive boot sector. I found that this happens due to big (52GB) third partition. If I disable it in boot menu - there is no delay.
Hardware CS MK2 060 128 MB, using original A4000T SCSI and SCSI2 SD with 64 GB SD card.
Partitions: 2GB, 10 GB and 52 GB.
OS: 3.1.4 with update 1 Kick: 3.1.4 Filesystem: FFS from 3.1.4 update 1 Maxfiletransfer: x1FE00