BE WARNED: do no use the CHECKALL.CMD ... or use it at your own risk.
The problem is with the /T parameter. From the docs:
/T Use this switch to enable the disk scan function of CHECKINI.
This will amongst other things repair non-functioning Startup
folders.
NOTE: THIS SWITCH SHOULD NOT BE USED IF YOU HAVE MORE THEN ONE
VERSION OF OS/2 INSTALLED ON YOUR SYSTEM.