jointer's wont square up cuts, shave the surface. If theres any dips they can remove those as well.
Unfortunately if youre not getting square cuts, its either you pushing the piece through wrong or the saw is set incorrectly, or both. Check to see that the piece stays against the fence the entire length, the whole way through the cut. I know sometimes the piece will want to pull away from the fence towards the end of the cut.
Until you get that right, you can easily re-square with a router, which will also leave you a better final cut.