This issue has been driving me a little nuts for months and I thought it was just my machine(s).
Am glad (sort of) that others are experiencing the same problem...!
Also using nnCron Lite 126.96.36.199 and a (single) weekly task specified in the cron.tab file:
30 10 * * Mon ~"C:\WINDOWS\system32\wscript.exe" "C:\myscript.vbs"
On very rare occasions nnCron fires the scheduled task again within a minute of the 1st fire.
I've only seen it on WinXP machines but that's only because I'm not running it on Win7/8 (yet).
Hopefully the developers can re-produce and fix...
Happy New Year!