I think you will need the latest ACPI driver from the ArcaNoae website. Don't ask me how to replace the existing one in the installation CD. Maybe you need to install a tool under Windows and update the ISO file to contain the new ACPI driver.
Another option that I basically took was to install under an old PC (because I still had it when I bought the new one), update the installation with the latest drivers, rip out the disk and place it into the new PC.
There are an increasing number of systems that have highly broken BIOS code.
The reason is obvious: systems like >= Windows 7 or Linux make only very little use of the legacy BIOS, with a tendendy to move to UEFI only (that means: no more legacy BIOS at all).
With OS/2 you are stuck with a kernel that is > 20 years old. It therefore makes considerable use of the BIOS, especially (or even exclusively ?) on system start.
The latest ACPI driver works around many BIOS issues seen in today's hardware. If Blue Lion eventually releases an install CD you should consider using that instead of eComStation 2.2beta.
Lars