SF 040 Loops and Perimeters

Before I switched to SF 040, I was using SF 035. When it did extruded loop and perimeter, there was no pause and the extruder stepper ran continuously. Now, with SF 040, it pauses at the end of the loop, retracts and restarts the filament and then continues with the perimeter. This new way results in more bumps on the surface than the old way since the retract/restart is not always perfect. Is there a way to control this and make SF 040 behave like 0435 and extrude continuously when going from loop to perimeter?

I think I found the answer to my question. I turned off the Clip feature not really knowing what it did.

Another question about perimeters and loops.

When generating tool path for an object with many internal surfaces like Nophead's Polygonal hole test, and Skeinforge is set to Perimeters and Loop, it first does the outer perimeter, then it does the internal perimeters one by one until it gets to the last one. For the last one, it will do the perimeter and then continue to do the loop in one stroke. Then it will go back to the outer surface and do the loop, then the loops for all the internal surfaces. Changing the order to loops then perimeter does the same thing with loops being done first.

Since the extruder seems to never start at the exact point, this usually leaves a gap in each perimeter and loop. Sometimes, the gaps are at the same place so it leaves a hole. This poses a problem if one wants a liquid or air tight hole through the object. In this case, it would be better if SF does the perimeter and loop of each surface before moving on to the next one.

Is there an option or a way to make SF behave this way?