Bicycle Mechanics - Possible stupid question

i just upgraded my cannondale r6 cannondale px3 crank to a ultegra crankset they are were both triple, my front derailer is out of alignment now and wont shift through all the front gears, i am assuming this is normal because i am going from a non shimano to shimano setup. I am hoping this isnt a sign of something bad. THanks in advance for any help

Your chainline has been altered. Did you also swap out the B/B?

yup its not off by much maybe 1/2 or 1/4 inches, its on there pretty good.

i meant yup its a new ultegra bottm bracket and crankset, its probably 1/4 or less off. Should i assume this is ok?

To check your chainline, is your middle chainring 'in line' with the middle of your rear cassette?
You need to reset the limiting screws on your front derailleur...

should i loosen the cable and do it from scratch or just play with the screws?

1/4", if to the outside is a lot, and may use up all the extension the Fr der has.
Loosen the cable, open up the limit screws so they place no constraints on the der range of motion and see where things are. The der cage should be at least 1mm inside the chain when the chain is on the small CW and largest cassette cog. If more than this use the limit screw to move the cage to ~1-1.5mm from the chain on the inside. If the chain rubs the cage, there is a problem. Clamp the cable after taking out all the slack and see what the shifter does. If it can't reach the large CW then a shorter BB is in order. (Shift the chain to a mid range or small cassette cog first). Make sure the cable is fully seated into the shifter and any cable stops. Steve