depending on your distance from the subject I'd say f/11 would be a pretty good base point for portraits which include a bit of the surroundings.... I understand what you're saying about manual setting the shutter/aperture - could it maybe be that you've set one of the custom functions or menu settings such that the flash sync speed is at 1/250 sec? ... I use a 40d so I imagine many of the menus would be similar... there's an option to set flash sync speed in Av (maybe spills over into M?) mode at 1/250 sec, perhaps this is why it won't let you change the settings? that's my best guess as at 1/250 it would limit the amount the aperture could close down while still maintaining a correct exposure.

the alternative I would say, would be to set manual settings as you wish, force the flash up, and just play about with the flash exposure compensation, until it gives out strong enough light to compensate for underexposure created by shooting at, say, f/11, iso 100 and 1/250 sec... you should be able to push it up a bit but it may run the risk of the 'deer in headlights' look...

are you using the onboard flash? if so I'm in the same boat and trying to make the most of it until I can afford an off-board one..... so sometimes you might catch me playing about with coloured cards and old CDs poking out of blobs of blutac near the flash mount =D

hope it all goes well for you!
Adam

Adam Edwards Photography