Hard drive Issue Maybe?

Ok i built my pc myself with an asus p5e-vm hdmi board with an intel e8400 core 2 duo. 400w ps, 4gb's memory, nivida 9800gt 1gb card. also i have a factory 500gb hdd and then another 320gb hdd.

My problem is this. Right after the pc boots bios at the top left hand side of the screen there is a flashing hyphen for about 30seconds and then bam it goes into windows.

The reason i put this into the HDD section was because the 320gb HDD only says its a 48gb HDD????

All the help would be greatly appreciated!
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