The errors that is shows are not present in the Jointool log or the status log.
Below is the actual log file:
[2014-08-04 13:59:09,906 com.vmware.vim.jointool] Failed to find instance config at: "C:\ProgramData\VMware\VMware VirtualCenter\instance.cfg", assuming defaults
[2014-08-04 13:59:09,908 com.vmware.vim.jointool] Storage directory not found in instance.cfg.
[2014-08-04 13:59:10,051 com.vmware.vim.jointool] Initializing DB datasource from: vcdb with dsn: VCDB as user:
[2014-08-04 13:59:10,057 com.vmware.vim.common.vdb.VdbConfig] Config name=vcdb
[2014-08-04 13:59:10,057 com.vmware.vim.common.vdb.VdbConfig] Property file=C:\ProgramData\VMware\VMware VirtualCenter\vcdb.properties
[2014-08-04 13:59:10,058 com.vmware.vim.common.vdb.VdbConfig] Loaded url from props=jdbc:sqlserver://SVDBM12R01.cloud.abl.navy.mil;databaseName=VCDB;integratedSecurity=true
[2014-08-04 13:59:10,058 com.vmware.vim.common.vdb.VdbConfig] Overrides=
[2014-08-04 13:59:10,058 com.vmware.vim.common.vdb.VdbConfig] prop:password
[2014-08-04 13:59:10,058 com.vmware.vim.common.vdb.VdbConfig] prop:dsn
[2014-08-04 13:59:10,058 com.vmware.vim.common.vdb.VdbConfig] prop:username
[2014-08-04 13:59:10,252 com.vmware.vim.jointool] DB datasource initialized.
[2014-08-04 13:59:10,252 com.vmware.vim.jointool] JoinTool started
[2014-08-04 13:59:10,253 com.vmware.vim.jointool] Storage directory for LDAP instance: C:\ProgramData\VMware\VMware VirtualCenter\\VMwareVCMSDS
[2014-08-04 13:59:10,254 com.vmware.vim.jointool] Operation Mode: initialize
[2014-08-04 13:59:10,271 com.vmware.vim.jointool] Creating directory services instance VMwareVCMSDS
[2014-08-04 13:59:10,272 com.vmware.vim.jointool] LDAP port = 389
[2014-08-04 13:59:10,272 com.vmware.vim.jointool] Base DN = dc=virtualcenter,dc=vmware,dc=int
[2014-08-04 13:59:10,272 com.vmware.vim.jointool] Storage dir = C:\ProgramData\VMware\VMware VirtualCenter\VMwareVCMSDS
[2014-08-04 13:59:42,429 com.vmware.vim.jointool] Operation "Create standalone instance VMwareVCMSDS" failed: : Action: Create Standalone Instance
Action: Creation of standalone instance
Action: Create Instance
Problem: Creation of instance VMwareVCMSDS failed: AD LDS Setup did not complete because one or more LDIF files could not be imported successfully.
[2014-08-04 13:59:42,430 com.vmware.vim.jointool] Recovering from failed Operation "Create standalone instance VMwareVCMSDS"
[2014-08-04 13:59:42,430 com.vmware.vim.jointool] Recovery successful
[2014-08-04 13:59:42,432 com.vmware.vim.jointool] Execution error.