I use screw tops all the time, although I usually use a two-handed hand-held capper.
I tried using my buddy's single-lever bench-top capper but switched back to my capper after a couple bottles. The problem I found was the piece that fit directly onto the cap was a little too tight and when I removed the bottle, I had to work it out and ended up twisting the cap loose (so it was pretty much like re-using old caps). That's not to say it won't work for you. The capper I tried may have been abnormally tight (it's pretty old and has seen a lot of use, although it still does ok with pop-tops). Another thing you could try is when you take the bottle out of the capper, twist it clockwise so that you don't loosen the cap.
Without seeing your capper or bottles, I can't really say. Have you tried capping a few empty to see how it does ?