Windows XP won't boot properly after a battery replacement

My computer clock has been acting up for a few days now, losing track of time constantly. When I booted it up yesterday, it gave me a handful of options just to get into Windows XP. The only way I could actually get into the OS was by using Safa mod. So, today I decided to try a different approach. I booted it up in Safa mod again, snapped some photos of all my settings in the BIOS, and then shut everything down. I swapped out the CMOS battery, fired the machine back up, and saw the message saying the CMOS had been cleared. I hit the Delete key, went right into the BIOS, reset the time, double-checked that all my settings matched what they were before, navigated to the Save menu, and hit enter on 'y' for yes.
The headache is that I still can't boot into Windows normally; it’ll only let me in via Safa mod.
The PC is about 6 years old. It runs pretty smoothly otherwise, and I'm certain there aren't any viruses or anything weird messing with things.
If anyone has a clue what might be causing this, I'd really appreciate the help.

Technically speaking, you don't even need a battery on the motherboard for the computer to actually boot up. The only thing you'll miss out on is having the correct time and date displayed.
Why not try pulling the battery out entirely and seeing if the machine starts without it?

Your issue might not even have anything to do with the battery at all.

I'm starting to think the battery actually isn't the culprit here.

If your system clock is off by minutes, hours, or even days, it won't cause issues with Windows.

The problem lies elsewhere within Windows—malware, faulty software, a corrupted registry, the hard drive, the power supply, and so on.

...I mean, I highly doubt you actually captured every single BIOS setting... we're talking like 20 different screenshots there... and that's assuming you even used the "Y" key to save them all.
You should probably track down someone who actually knows their way around this stuff to take a look...

I’ve got nearly 20 screenshots of my BIOS settings saved. My watch is running perfectly today, so I’m pretty confident I nailed the configuration in the BIOS. I went through the routine to save the data, it asked me if I wanted to proceed with 'y' or 'n', I hit 'y' and Enter, and then I was out. Honestly, there might be a little glitch in what John Turner34 wrote earlier.
I ended up taking my computer down to the local repair shop.

...on my end, I have to hit the Z key just to select "Yes"... since the layout won't be properly set for an American keyboard until after the system finishes booting up, I was being a little extra cautious about it...

Same here. When I realized my 'y' key had quit on me, I just gave the 'z' a squeeze instead. :-)
I actually learned something new today. And hey, hopefully this helps anyone else out there dealing with 'z' or 'y' issues.

My computer is finally back in action!
The graphics card died on me, and honestly, the motherboard was looking pretty rough too. It’s about six years old now, so I guess it’s earned its retirement, right? They tried reinstalling Windows, but that crashed immediately, so the techs had to dive in and test every single component one by one. Turns out there were a few other little glitches they managed to iron out while they were at it. Even my integrated network card—which hasn't worked for ages because of some weird hardware overlap—is suddenly working perfectly. Everything is running smooth as silk now.
I really shouldn't give them free advertising, but man, I got such a great deal.