Final Fantasy vi/pokemon sapphire problem

My VisualBoyAdvance that I've been using for quite some time, has up and decided to pitter out right in the middle of final fantasy vi. I know that this doesn't work like a regular GBA, it's a program, but it's like it decided to break. I didn't use ANY cheats, I saved properly, I made sure I shut down the computer properly; I didn't change ANY settings, and I shut it down yesterday, properly.
I woke up, did my work, had a decent day; start up the computer, listened to some music, stopped the music and started up VBA 1.8.0 (beta 3)
Load...
Final Fantasy VI Advance (Xenophobia)
Error reading image C:\...(for my and your benefit, basically the file path)
...VBA\roms\Final Fantasy VI Advance (U)(Xenophobia).gba
...
...
is anybody here familiar with "'FFFFFFFFFFUUUUUUU-' comic"?
I just wanted to play Final Fantasy VI Advance (U)(Xenophobia).gba, that's all I wanted.
Am I hacked? Is that what's going on?!
Could anybody please give me an idea of what to do?
I would appreciate this very much.How Pokemon sapphire plays into this is I was able to play it about 9-months ago, but I now cannot play it. A simlar message appears, only difference is it's about pokemon sapphire.
What is going on?

Did you tried to run the game through the Recent function?(File -> Recent)
If yes, try running the game using the 'File -> Open'.

This happened to me when i was like 8, yes do try what meganova said.

I wouldn't rely on a PC based emulator to run games like Final Fantasy or Pokemon. Ive had the emulator crash when I was saving the game in Emerald after playing for 3 hours.

I almost never use "recent", and it's not something simple, otherwise; I would've fixed it myself.
It turns out yesterday, all I was looking for was an esper list to make sure I didn't miss any. Checked out GameFAQs.com under the advanced version, no esper list.
Did I check FF3 SNES on GameFAQs? Hell no.
So I go google-ing, and I run into a GameFAQs leech-site, unwittingly. It was the GameFAQs SNES version of FF6(J)/3(U), esper list, and I copy-pasta'd it, saved it.
3 Avast! full computer scans earlier today...
Turns out son-of-a-gun virus just ate a few new assholes in my computer.
It is ridiculously sluggish, and Many many files of varying importance were completely destroyed, and/or damaged beyond repair.
Final Fantasy vi happened to be one of those files.
Pokemon Sapphire was broken before I downloaded it from here; the original Sapphire file got deleted on accident.
Either way, this whole little black IBM Thinkpad laptop... is completely F#$%ed, and it turns out I gotta' get it "scrubbed".
A shitload of files from... prettymuch all parts have this message when scanned: "Unable to be scanned: the system cannot read from the device."
Ain't that some BullSpit?
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Also, I don't have much choice in the emulate-Final Fantasy issue 'till I get workin' here soon.
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but don't feel bad for me, I have 2 other computers that work fine. For now...
One of those two, is pretty-much impenetrable to viruses.
The only thing: the save is from 2 days before I run into Setzer(Drakla in my game), and head to get the "Falcon". I was back to right after you follow a familiar looking fellow named Gerad(Yes, he's Edgar), on a boat.