Managed to get it working again by adding the ModInstallPath registry manually. Thanks dopefish for the awesome program, makes life so much easier. :D
Edit: As for the registry, you could probably call TF2 install directory from here?
Code:
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINESOFTWAREWow6432NodeMicrosoftWindowsCurrentVersionUninstallSteam App 440]
"DisplayIcon"="H:Steamsteamgames\033bdd91842b6aca0633ee1e5f3e6b82f2e8962f.ico"
"DisplayName"="Team Fortress 2"
"HelpLink"="http://support.steampowered.com/"
"InstallLocation"="h:steamsteamapps<user>team fortress 2"
"Publisher"="Valve"
"UninstallString"=""H:Steamsteam.exe" steam://uninstall/440"
"URLInfoAbout"="http://www.valvesoftware.com/"
"NoRepair"=dword:00000001
"NoModify"=dword:00000001
This probably only works for 64-bit version of Windows. The 32-bit version may not include the Wow6432Node in the registry. I won't know though.