Windows 7: Weird boot up black screen with cursor problem?

Ive posted this in other blogs looking for a fix but its a strange one I cant figure out and Ive been tweaking computers since the Commodore Vic 20 days. ...
Ok at boot up on my self built machine after the initial windows 7 logo I get a black screen with movable cursor. Its sort of started about 2 weeks ago after I started using a hdmi cable for my second monitor.DVI for my main screen. Ive tried re installing windows both ways keeping files and a format re install and its still doing it. To get around it I have to boot into bios and change my boot sequence to another hard drive (I have 3,one with Windows 7 on it). When I change it to boot from another hard drive naturally it says bootmgr missing hit shft control alt del to restart. So I do and then go back into bios and change it back the way it was booting to the hard drive with windows 7 on it and it starts right up like everything is normal. It runs just fine after that, plays games,apps internet everything is normal. But when i shut it down completely and start it fresh it goes back to black screen with cursor again. Ive never had this problem but there is alot in this online. I have all the latest drivers including video driver 10.7 ATI. This is strange It must be something to do with using a HDMI out or video driver related I think. I cant find any viruses or spyware and no other conflicts with any device. No usb drive is attached. Also I can load into safe mode too thats not an issue. Anyone know whats the deal?? Thanks for your help!