Orbmiser ~ I think you are onto it there! It never mattered in Mac OS or Windows, I did had floppy 3 mode disabled and just figured that was for a floppy drive, but noticed above that there was a drive A setting in the BIOS for different sizes. So after you said that and I went back into BIOS I noticed it Drive A support was set for 1.4M ( I believe that was what the old floppy disk held), then I looked over to the left pane and noticed it did in fact have choices so I entered the setting and chose no floppy drive, saved to CMOS and so far no floppy window popping up. So I guess we can close this one out as SOLVED.
I Thank You very much for the heads up!
OS: Linux Mint 16 KDE
Motherboard: Gigabyte EP45-UD3P Rev. 1.6 FE BIOS
CPU: Intel Core2Quad Q8400 2.66 GHz.
Memory: GSkill: 4 GB DDR2 800 MHz.
GPU: PCI-E 3 NVidia GEFORCE GTX 650 DDR 5, 1GB Ram
Drives: Int: 500 GiB WD HDD, Ext: USB 2 500 GiB HDD