The 'kLIBC Pathwriters' that I installed (klibccfg_1_0_2_1.exe) did not added TEMP, TMPDIR, LOGFILES on the config.sys.
I add those manually and the D: drive issues are gone.
Strange. I've just checked the installation .wis script. It contains:
REGISTERCLASS="kLIBCConfig|$(1)\klibccfg.dll"
CREATEOBJECT="REPLACE kLIBCConfig|kLIBC Pathrewriters|<WP_CONFIG>|OBJECTID=<WP_KLIBCPRW>"
CONFIGSYS="SET LIBC_HOOK_DLLS=$(1)\klibccfg.dll@_kLIBCInitPath!pathrewrite"
WRITEPROFILE="$(ETC)\klibcfg.ini\REWRITE\/etc|%ETC%"
WRITEPROFILE="$(ETC)\klibcfg.ini\REWRITE\/var/log|%LOGFILES%"
WRITEPROFILE="$(ETC)\klibcfg.ini\REWRITE\/tmp|%TMP%"
That looks as if it should have added the CONFIG.SYS entry and created %ETC%\KLIBCFG.INI.
Apologies for restarting this thread, I have essentially the same problem. But with slightly differing results. I have a very full popuplog.os2 file with lots of ANPM.EXE and REXXAPI.DLL errors...

ANPM is on C:, but I've setup and wanting UNIXROOT to be on D:.
I'm not even being asked if I want config.sys fixed but it does inform me that it's modified config.sys (it hasn't).
Which makes me wonder if there is an implicit assumption here that all of the packages are on the one singular drive (ie no reference to UNIXROOT)?
Thoughts?