Help!! Defense+ Behaving Weirdly!

I’m using CIS 5.9 on Windows 7 Ultimate 32-bit.

The story goes like this.

I’m using Safe Mode for Defense+ and Custom Policy for Firewall.
All the while it was working fine and nice. But one day (in fact, just a few days ago), it started alerting me and asking me for permission regarding things that shouldn’t even have popped up!

For example, I use XnView to view animated GIF files. I double-clicked on a GIF file and Defense+ alerted me saying that explorer.exe is trying to open xnview.exe, which is ridiculous because explorer.exe is trusted (and I’m on Safe Mode, so that confused me even more), and xnview.exe is something I’ve already allowed and remember-my-answer-ed.
All of my other previously allowed applications and even Windows’ files could cause Defense+ to alert me.

Later on, I looked into the Defense+ Computer Security Policy, and discovered that the entire bunch of files under the categories of “Windows System Applications”, “Windows Updater Applications”, “COMODO Internet Security”, “All Application”, as well as the line “%windir%\explorer.exe” are all missing!! Certain previously allowed programs are also missing.
In addition, some allowed programs have repeated rules (because Defense+ asked me again and I selected “Remember my answer” again), so I think Defense+ ignored the rules.

Not long after, less than half a day, my Windows 7 could not start anymore. After turning on my computer, and the BIOS did all its stuff, it stuck there at the line “Verifying DMI Pool…” or something, and nothing loaded anymore.

I’m now on another Windows 7 of my system. (I have 3 Windows 7 installed separately in 3 hard drives.)

I couldn’t figure out why this happened, because I wasn’t doing anything weird or out of normal. I was only using my computer normally, and my Avira antivirus didn’t catch anything funny, nor did COMODO Firewall and Defense+. (I disabled CAV.)

Please enlighten me. In the worst case, I may have to reinstall my Windows 7 from scratch, but I don’t want the same thing to happen again so I need to know what caused this.

Thanks.

" I’m now on another Windows 7 of my system. (I have 3 Windows 7 installed separately in 3 hard drives.)"

3 hard drives ? Or one hard drive with 3 partitions ? 3 copies of Windows 7 on one PC explain why ?

Not 3 partitions.
3 hard drives.

I have 3 hard drives. Each hard drive I installed 1 copy of Windows 7.
This is for backup, in case the main Windows 7 goes wrong and cannot be accessed. With more than 1 copy of the OS, I can still access my data and manage them before doing whatever is necessary next.

If I only had 1 Windows 7, I wouldn’t even be able to ask for help here anymore.

And now, what I worried most has happened.

Can you see the broken Win 7 with Explorer from one of the other Win 7 installations?

Download Speedfan and read the SMART parameters of the affected drive to if the drive reports it is healthy or not. Also run a scan tool of the HD’s manufacturer for a more in depth analysis to see if it is fit or not.

Then scan the affected drive with various scanners for malware:
Hitman Pro
Malwarebytes Anitmalware
Super Antispyware
CIS