Check to see if your x:\\os2\\boot\\ibmkb.sys , \\kbdbase.sys, and \\mouse.sys look reasonable. Look with an editor and see if it indicates that they're OS/2 files. It sounds to me like something got overwritten or corrupted.

Does your bad config.sys have the proper BASEDEV and DEVICE statements?

BASEDEV=IBMKBD.SYS

DEVICE=x:\\os2\\mdos\\vmouse.sys
DEVICE=x:\\os2\\boot\\mouse.sys serial=com2

DEVINFO=KBD,US,x:\\os2\\keyboard.dcp

That's about all that seems relevant from my Warp 3 Connect config.sys. eCS may have different names.

Best of luck.

Cheers,
Scott.