Yes, ConfigTool uses large ini files. (CFGTOOL.DAT is an OS/2 .ini file.)
The summed size of all .ini files opened by the PM Prf functions seems to be limited. Therefore usually one can't open a second OS2.INI after having used the system a bit. That might apply in your case as well.
I made the experience that the system gets unstable if the size of the WPS handles in OS2SYS.INI exceeds 4 blocks. The OS2.INI is the larger file and seems to grow with that, too.