Got it. This should happen with 0.3.0 too. I suppose that the device lowers its speed and that it takes more time to prepare the wlan0 interface when it is down. I didn't have this problem because I was always connected to wlan.

To fix this edit /usr/lib/pymodules/python2.5/wifieye/scan.py and:
a) add "import time" at the beginning, along with other imports
b) find the line "subprocess.call(["/sbin/ifconfig", iface, "up"])" and after that (before the try) add the line: "time.sleep(0.3)". Be sure to use the same number of spaces as the other lines.

It will make the graph more slow but it will not have gaps.