"Invalid partition table" when booting system

I have a Dell Latitude E5430 laptop. I have replaced the CD drive with SSD. Then I partitioned both disks, They both have msdos partition table with two primary partitions. No flags on the partitions. I installed GRUB on SSD and it runs a nixOS system from one of the partitions on SSD. The partitions on HDD are used as /home and /var.

My problem is: when booting I get a "Invalid partition table" message (just it, black screen besides it). After I hit Enter, the system will boot normally, so this is more of an aoyance, than critical problem. I have edited the boot sequence in BIOS, and disabled everything except "drive bay".

My questions: Where does this message come from (BIOS or GRUB). How can I squelch this message or at least how can I debug and see what is the exact problem with my partition table?