For your first run, you are putting your thumbs on black keys, and that will always make it choppy. Avoid using finger 1 or 5 in either hand for a black key. This may mean starting on a different finger or crossing under/over more often.
Also on that first run I notice you aren't crossing under/over at all in either hand. Keep in mind that if you end on finger 5 in the RH or finger 1 in the LH when playing either a scale or arpeggio, you're pretty much done for and are forced to "jump" the whole hand. That's why you're having trouble with accuracy and making it sound smooth. You need to cross the thumb under in the RH on the way up before you get to using finger 5. An example of this might be (I don't have the music in front of me to try it) 1-2-3-4-1 etc. as opposed to 1-2-3-5-1. Your thumb under the 4th finger can make that a lot smoother as you can play it pretty much legato throughout and no jumps necessary.
LH looks like it starts on a black key, so the fingering might be 4-3-2-1-4 etc. where finger 4 crosses over the thumb. You might still have a little leap here between finger 1 from the first octave and 4 on the next part of the run, but the crossing over will minimize it.
I'm not sure if that is the exact fingering however, as it all depends on where the black keys lie. If you can provide a copy of the music with the measures in question I might be able to give you more concrete fingering suggestions.
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