Ever since I rooted out some malware from my dad's account, the computer has taken to being delayed after logging on.

XP Home SP3.
Boot up to log-in screen is fine.
Entering password to desktop is the problem.

After entering the password, the screen goes to the desktop. It's at this point it seems to pause. Wallpaper only - no taskbar, desktop items etc. Pressing the windows key doesn't bring up the start menu. It pauses for about 40-50 seconds, then carries on without problems. Desktop loads up and I'm ready to run.

Strangely, this happens only after a hard (or cold) boot. A soft reboot (windows->shutdown->restart) has no problems.

I've fiddled about with processes that might be causing problems but can't see anything obvious - I've been into msconfig and nothing untoward in the menu. I've been to the services, hidden the windows services and disabled all non-windows stuff but still happens.

I've run hijackthis and my other antiviral/malware programs and there's nothing to detect. I've run CCleaner's registry fix but nowt.

I thought it was stuff on my dad's account (he has the GameHouse games like bejewelled etc), so backed up his stuff, deleted his account (still had a problem), recreated a new account and again, no change. Not restored his stuff yet. Before the viruses were discovered, it was working fine. Avast found some viruses which it could remove and some which it couldn't. Ended up taking the hard drive out and used a USB caddy to scan it as an external drive, which was fine. It was after removing all of the malware when the issues arose. My dad could log into his account but it would freeze. Everybody elses account was fine. Now everyone's account seems to be affected.

Any ideas?

check the start up menu and see if anything is trying to start which may have been removed during the clean up
also disable system restore when the system has been restarted enable SR and create a new restore point
this is to ensure no nasties are lurking/hiding within SR

There's nothing in the startup folder itself, and the processes are all legitimate.

I've hated system restore and hence it should be switched off. Will double check though.

Are there any system events in the event viewer that can shed some light on the problem?

Wouldn't it be quicker to just back up his data and re-install Windows, (wiping the drive in the process)?

It's also get rid of any trial software, or apps which he doesn't use any more...
That's what I'd do, simply because life is too short to waste it trying to fix Windows* problems.

* Or Linux. Or OSX. Or <insert other Operating System name here>.