Does the application really run on OS/2 or it's just a DOS app?
I haven't found anything special in the CONFIG.SYS. The only additions seem the be
LIBPATH=...D:\PEP\DLL;
RUN=D:\OS2\SYSTEM\HYBERSET.EXE
Or is this caused by the installed bonupak apps?
At least the OS/2 driver for the Digi AccelePort Digiboard ISA card should have an entry there, I guess. A DOS driver exists for this card and DOS accesses the card independent of the host OS. The same applies for a 3Com 509 ISA network card.
I had for multiple years a PDP-11 emulation with an ISA Osprey CPU board and DOS software, an ISA Digiboard and an ISA 3Com 509 nic running, first under W95, then under eCS. I'm happy that the emulation on the current system has moved almost completely to software. Also the multiple serial ports (we could drop that down from 16 avaliable to 8, with 5 ones in use) have a driver for the host OS (unfortunately W7), but for the 4 data buses we had to use special hardware from Startech, because of timing issues with others.