It's never hard to find reasons to not do something out of the mainstream.  What were your reasons for switching?

I am not even a Windows user, would be happy to never use Windows,  haven't used Windows on a regular basis since Win95 in the 90's and I don't recall much trouble in getting Colemak working fine in WinXP on VMware Fusion on my Mac.  Of course, my reasons for having it were compelling enough to me that whatever difficulties I may have had were not enough to deter me from getting it done.

It's fine that you don't feel it's worth the trouble, but it's all in the reasons you have for doing it.

I'd wager that 80% of young men 'are better than 95% of the population'. The maths don't quite add up on that one.

Be that as it may, I don't think it's more trouble than it's worth if you think about it. How much time will you be spending typing through your lifetime versus the initial investment? To me, the answer is 'so much that even a minor improvement will be worth a lot of effort'. And to me it's been more fun than hard work anyway.

I second Simonh: At first, try it out with PKL. I use that even on my main machines now! You just need to put a shortcut to the binary in your Startup folder and it'll run automatically. PKL doesn't work with absolutely everything but it's perfect for most things.

Windows logon? Well duh, you should see that one coming. I make my passwords so they're layout invariant to be on the safe side, but it's not that hard to avoid the problem in other ways if you're more than moderately 'tech savvy'.

Jl: If you're not ready for a great life hack, don't sweat it. You're in good company. But don't diss it more than it deserves before you've actually tried it for real.

Otherwise, see my BOARD WARS picture...   ;)

My laptop has a fingerprint scanner which has made the login problem null. Not that a QWERTY password really bothered me; I didn't change my keys from QWERTY or anything.

If you can't fix this problem, why not turn it to your advantage? Use the Qwerty layout whenever you are setting or entering system passwords, but hit the keys as if Colemak were running.

E.g. Suppose you want to use "MyPassword".
Typing that in Colemak while the Qwerty layout is active results in: "MoRaddw;sg"

Voila, you've not only solved the problem, you've turned a crap password into a pretty secure one that is easy to remember and type in.

The layout in effect when you're trying to unlock your Windows machine is the same as your logon layout (i.e., QWERTY), regardless of what the layout is once you've unlocked.  And if your logon layout is QWERTY, Rajagra's suggestion is a valid (and epiphanic) approach.  You will not pay a penalty when unlocking.

Yes, I have an XP box at work for which lockout layout is definitely QWERTY, the logon layout.  Learned it the hard way after trying to unlock by painstakingly typing my (non-layout-invariant) password in Colemak, and realizing with some relief that that wasn't necessary.  I only needed to learn my password in one layout, even if that layout wasn't Colemak.

Layout-invariant passwords are probably OK for home use.  For work, they curtail one's choices pretty drastically by taking many letters out of play: f p g j l u y ; r s t d n e i o k.  Especially hard when policy dictates you have to change passwords periodically.

Finally: If you are going to use a layout-invariant password, never ever advertise it so blithely!  Colemak is not a backwater anymore, and you're just making life easy for a savvy cracker by willingly shrinking your pool of passwords.