i actually did created them in the side view
How are you creating the bones(set bone tool to default). You should not create bone in perspective vuew.............dave
I actually created the joint chain in side view..the perspective view image was just for reference so you guys can really see what is going on..I did reset everything..I even deleted the prefs folder and let Maya create a new one but in vain..the funny part is that it was working fine maybe a day before..I even reinstalled Maya but still doing it
I have a problem with Maya joint tool. Every time I create a joint chain the bones are not represented right. they should be connecting the successive joints but instead they are oriented in a different plane at around 90 degrees angle. Even when i use the skeleton generator i run into the same problem. I checked the settings and i think they are at their defaults. I don't know if this is related to Maya or that is me setting some wrong..But i reset Maya to its default and still have the same problem..i even reinstalled Maya in vain.. i attached screenshots of my viewports to illustrate the problem and also of my joint tool settings 
