Ok, I ran /scripts/upcp --force as you suggested and saw errors related to Net::AIM, which I re-installed 3 times both in WHM and SSH. Also errors for an assortment of issues, including DBD::mysql (which I also reinstalled earlier). Here is a sampling at the tail end:
=> cPanel Install Complete
==> Removing Installer.....Done
==> Starting cPanel....
Waiting for cpaneld to shutdown......Done
Waiting for webmaild to shutdown......Done
Waiting for cppop to shutdown......Done
Waiting for cppop-ssl to shutdown......Done
Shutting down Mailman's master qrunner
mailmanctl: no process killed
Waiting for cpsrvd to shutdown.......Done
Waiting for cpsrvd-ssl to shutdown......Done
Waiting for whostmgrd to shutdown......Done
==> SMTP Mail protection has been enabled. Only users with the gid mail or mailman may make smtp connections.
(internal death) Mon Jan 16 10:00:42 2006 [14537] error: Can't load '/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mysql.so' for module DBD::mysql: libmysqlclient.so.10: cannot open shared object file: No such file or directory at /usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229.
at /usr/local/cpanel/cpanellogd line 60
DynaLoader::croak('Can\'t load \'/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thr...') called at /usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229
DynaLoader::bootstrap('DBD::mysql',2.1021) called at /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/DBD/mysql.pm line 14
require DBD/mysql.pm called at /usr/local/cpanel/cpanellogd line 60
main::BEGIN() called at /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/DBD/mysql.pm line 0
eval {...} called at /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/DBD/mysql.pm line 0
(internal death) Mon Jan 16 10:00:42 2006 [14537] error: Can't load '/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mysql.so' for module DBD::mysql: libmysqlclient.so.10: cannot open shared object file: No such file or directory at /usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229.
at /usr/local/cpanel/cpanellogd line 60
Compilation failed in require at /usr/local/cpanel/cpanellogd line 60.
main::BEGIN() called at /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/DBD/mysql.pm line 60
eval {...} called at /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/DBD/mysql.pm line 60
(internal death) Mon Jan 16 10:00:42 2006 [14537] error: Can't load '/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mysql.so' for module DBD::mysql: libmysqlclient.so.10: cannot open shared object file: No such file or directory at /usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229.
at /usr/local/cpanel/cpanellogd line 60
Compilation failed in require at /usr/local/cpanel/cpanellogd line 60.
BEGIN failed--compilation aborted at /usr/local/cpanel/cpanellogd line 60.
Can't load '/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mysql.so' for module DBD::mysql: libmysqlclient.so.10: cannot open shared object file: No such file or directory at /usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229.
at /usr/local/cpanel/cpanellogd line 60
Compilation failed in require at /usr/local/cpanel/cpanellogd line 60.
BEGIN failed--compilation aborted at /usr/local/cpanel/cpanellogd line 60.
[a fatal error or timeout occurred while processing this directive][a fatal error or timeout occurred while processing this directive][a fatal error or timeout occurred while processing this directive]Waiting for cppop to shutdown......Done
Waiting for cppop-ssl to shutdown......Done
Can't load '/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mysql.so' for module DBD::mysql: libmysqlclient.so.10: cannot open shared object file: No such file or directory at /usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229.
at /usr/local/cpanel/bin/eximstats line 260
Compilation failed in require at /usr/local/cpanel/bin/eximstats line 260.
BEGIN failed--compilation aborted at /usr/local/cpanel/bin/eximstats line 260.
Waiting for cpsrvd to shutdown......Done
Waiting for cpsrvd-ssl to shutdown......Done
Starting Mailman's master qrunner.
==> Starting SSL tunnel...
==> Start Melange Chat Services...
Content-type: text/html
entropychat 0.2.6 started
<br>Listening on port 2084...
==> Post Install Complete
Broadcast message from root (Mon Jan 16 10:00:49 2006):
cPanel Layer 2 Install Complete
Updating addon type:scripts addon:phpBB version:2.0.19-1.0.......Done
Updating addon type:scripts addon:AdvancedGuestBook version:latest......Done
Updating addon type:modules addon:addonupdates version:0.5.......Done
Updating addon type:modules addon:cronconfig version:0.4.......Done
Added Contact
[email protected]
Rebuilding Process List...Done
Scanning for new mail senders.....Done
Scanning suexec_log...Done
It seems as though cPanel is unaware of software I have installed for some reason.