I don't see why it can't be done. Can you post the file and a clearer idea of what is being cut where?
As dunlea421 said, SCAL doesn't like single lines, it wants closed paths. If you create single lines and try to cut them, SCAL will connect them in an attempt to close the path. So if your design has single lines, rather than a closed path, it will cut its way from one line to the next, even through that is not what you intended.
What you need to do when you want to put a line out by itself (such as for a slit), is to create a DOUBLE line that is a closed path. That way it cuts over itself twice, but looks like a single line.
I'm sure there are much easier ways to do it, but this works for me. I don't have illustrator, so hopefully you can figure out the equivalent.
In inkscape, select the 'Draw Beizer Curves and Straight Line' tool - the one that looks like an inkpen, not the pencil. I then create a double line that is a closed path by clicking to make the first node, pull away to make the line, click to set the second node THEN GO BACK TO THE FIRST NODE and double click on it. (The purple thing is my representation of the inkpen tool.)
If you just need a straight line, you are done. If you need a curve, read on.
This will give you 2 lines on top of each other that are connected at the end. Next, grab the line with the node tool and create the curve you would like - only ONE of the lines will move at this point. Fix the curve the way you want it, ignoring the straight line.
Next, you want to make the second line that is still straight to match the first line. If the node handles aren't already showing, click on the image again with the node tool to make them appear. Now move the node handles for the straight line until they are directly on top of the node handles for the curved line by matching up the circles on the ends.
You will now have a curved closed path that will cut as if it were a single line. Hopefully, this is what you need to know and it makes sense.
