Hi,
What all PCIe adapter you have installed in the Slot 1, Slot 2 and slot 3?
Have you checked by updating BIOS and ILO to latest ?
Also reconfirm issue with PCIe slot 2/slot 3 ?
Can you please remove any adapter installed on the Riser 1 (Slot 1) and then check the same in slot 3 ?
Any specific adapter not detecting ? can you please share its specification?
Quickspecs
https://h20195.www2.hpe.com/v2/getpdf.aspx/a00008159enus.pdf?v
also
Check Standard riser options at page 10
NOTE: If secondary full height kit is installed, then primary PCIe Slot #2 cannot be used. Only 2 full height slots are supported
Refer Gen10 Riser options
https://assets.ext.hpe.com/is/content/hpedam/documents/a00043000-3999/a00043229/a00043229enw.pdf
Regards,
Sudhir