Are "Webmail" and "phpmyadmin" available in the module "Features"?
ISPmanager uses the OS repositories. Sometimes some applications aren't available in standard repositories(in this case you have to add additional repositories), If they aren't available in yum (in CentOS) they are also not available in ISPmanager.
You should try to add new repositories and execute:
/usr/local/ispmgr/sbin/pkgctl cache
killall ispmgr
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