I did exactly the same. I was so busy learning lead that I neglected rhythm, and for ages it caused me problems.

What did I do? learned Bass - which helped massively on concentrating on rhythm and playing simple lines in different times. I also went on to drums, which reinforced it and is brilliant fun, but it was the bass that really sorted my rhythm out for me.

Also, if you already play guitar the notes and hence scales are all the same (well, on a 4 string bass tuned to EADG anyway).

Final thought on guitar - get your hand moving consistantly in quavers down/up/down/up... that way it's easy to hit or miss beats as necessary and syncopation just gets stuck in your head as 'up/up/up'...